Re: [gmx-users] Using Charmm 36 forcefield on Gromacs 4.6 or higher
Hi, just try to disable OpenMP threads, unsetting OMP_NUM_THREADS environment variable Francesco 2013/8/1 akk5r ak...@virginia.edu Hi All, I am trying to run a membrane protein simulation on Gromacs 4.6 using the Charmm 36 force field parameters. I found the following parameters on the gromacs mailing list for Charmm 36: *; nblist cut-off rlist= 1.2 ; long-range cut-off for switched potentials rlistlong= 1.4 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.2 ; Relative dielectric constant for the medium and the reaction field epsilon_r= 1 epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = switch ; cut-off lengths rvdw-switch = 0.8 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No * Putting these setting into my .mdp file, I then get this error on grompp: *ERROR 1 [file nvt.mdp]: With Verlet lists only cut-off LJ interactions are supported* I then turned off the Verlet cut-off scheme and was able to create a .tpr file. Then I ran my .tpr on mdrun and got the following error: *Program mdrun, VERSION 4.6.1 Source code file: /home/akk5r/Downloads/gromacs-4.6.1/src/kernel/runner.c, line: 824 Fatal error: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors* At this point, I don't know what to do. I have to run this job on a cluster system due to the size of the system. Does any one know how to run Charmm 36 simulations on Gromacs 4.6 or higher using Verlet cut-off scheme? Best Wishes, Ali -- View this message in context: http://gromacs.5086.x6.nabble.com/Using-Charmm-36-forcefield-on-Gromacs-4-6-or-higher-tp5010290.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Oteri Francesco, PhD https://sites.google.com/site/francescooteri -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to describe the change of channel in the MD
Hi, you can use CAVER (http://www.caver.cz/) to detect tunnels. In the first case you should not see anything while in the second you shold see a channel.An other program you can use i s MDPocket ( ' http://bioserv.rpbs.univ-paris-diderot.fr/fpocket/): It simply detects cavities (either tunnels or closed cavitiies) and outputs informations. I successfully used these two software to characterize tunnels and cavities in a MD simulation. Francesco 2013/6/19 aixintiankong aixintiank...@126.com Dear, In the MD, I find that when the ligand keep in the active site , the channel formed by two loops is closed. without the ligand the channel is opened. I don't know how to describe the change of channel. could i describe the channel by calculating the the most narrow distance(mass center) between the residues on the two loops? please give me some adviece. thank you very much! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Oteri Francesco, PhD https://sites.google.com/site/francescooteri -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] fftw without SIMD
Dear gromacs users, I am compiling gromacs 4.6.1, but when I configure the package ccmake says: The fftw library found is compiled without SIMD support, which makes it although I compiled fftw ./configure --enable-single --enable-shared --enable-sse2 CC=icc F77=ifort CFLAGS=-msse4.1 Is it a known issue or I did something wrong? Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: REMD analysis
Hi to everybody, Bharat, maybe i didn't follow exactly the wole tale, but is it possible you are running xmgrace without the -nxy option? You are probably visualizing the data related the 1st replica several times! Francesco 2013/5/24 Mark Abraham mark.j.abra...@gmail.com On Fri, May 24, 2013 at 10:44 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Thank you for your detailed response to my query. I understood the concept of ordered arrangement of ensembles in replica_index.xvg. But I have a doubt, you said that *At time 4, replicas in ensemble 1 and 2 have exchanged. So replica 0 is now in ensemble 2, which is expressed by 0 in the third column* *of the third row of replica_index.xvg.* This is fine , as the output of replica_index is :- 4 12*0 * 3456789 10 11 13 12 But, i didn't understand this The same condition is expressed by the first column of the third row of replica_temp.xvg, where you will find 2, also expressing that replica 0 is in ensemble 2 at time 4. Here's the output for replica_temp . The first column third row is 2, its ok, but, its shows that replica 0 is in ensemble 1 instead of 2. No, if the rows of both matrices describe time, and there are two different matrices for the same exchange set, then the information described by a column must differ, like I said last email. You are applying the same interpretation to a column from either matrix. 4 2013456789 10 11 13 12 In addition to this, in my last mail I showed the temp graph for all replicas. (https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png) . Not all replicas visit all the temperatures, but some of them visit all the temperatures. Is it sufficient to move with the further analysis , as in some papers they show that some replicas visit all the temp which means that the sufficient sampling has been achieved. In my case this is true for some of the replicas and the average acceptance ratio achieved was 0.22 ?? I've answered this question several times. Each replica merely visiting each temperature means nothing for converged sampling. There's lots of literature here, including stuff by me ;-) A balance of replicas visiting ensembles is necessary but not sufficient for the kind of replica flow that would be necessary for generalized convergence. One can shrug one's shoulders at some point and say things are probably as good as they'll get for reasonable cost, but your reviewer might disagree with you. Convergence of sampling at a single temperature can be assessed in a similar way as for non-REMD simulations, caveat that the exchange events pretty much stop you using metrics based on correlation time. If you want to know how to do things properly, you need to do some reading. Mark On Fri, May 24, 2013 at 5:07 PM, Mark Abraham mark.j.abra...@gmail.com wrote: At time 0 we have an set of replicas and an (ordered) set of ensembles. We could label these however we liked, but for (in)convenience we use 0-(n-1) for both. The rows of the matrices in the *.xvg files change with time. At time 2, replicas in ensemble 0 and 1 have exchanged, so replica 0 is now in ensemble 1. At time 4, replicas in ensemble 1 and 2 have exchanged. So replica 0 is now in ensemble 2, which is expressed by 0 in the third column of the third row of replica_index.xvg. The same condition is expressed by the first column of the third row of replica_temp.xvg, where you will find 2, also expressing that replica 0 is in ensemble 2 at time 4. The columns of the two matrices allow you to see either the profile of which replica was in this ensemble at which time, or which ensemble this replica was in at which time. Mark On Fri, May 24, 2013 at 8:43 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I tried a lot to understand the meaning and relation between the .log file and relica_index file, but I was not able to break the code. I tried to look into gmx forum for some clue, but didn't find any. So, if possible can you explain it ... Replica exchange at step 1000 time 2 Repl 0 - 1 dE = -1.067e+00 Repl ex 0 x 123456789 10 11 12 x 13 Repl pr 1.0 .01 .68 .21 .05 .09 .26 Replica exchange at step 2000 time 4 Repl ex 01 x 23456789 10 11 12 13 Repl pr.91 .32 .00 .07 .18 .08 output of replica_index.xvg 0 0123456789 10 11 12 13 2 1023456789 10 11 13 12 4 1203456789
Re: [gmx-users] Conceptual question about the computational scaling of MD
Hi Andrew, maybe it is true on single processor simulations. It is false for sure when we talk about multicpu simulations because in this case each cpu has comunicate with each other and the implementations of this step makes a huge difference between the different codes. Francesco 2013/5/11 Andrew DeYoung adeyo...@andrew.cmu.edu Hi, Please forgive me for this slightly off-topic question. Suppose I use the particle mesh Ewald algorithm for the computation of electrostatic interactions. It is often mentioned in the literature that the PME algorithm scales as O(N logN), and that the electrostatic interactions are the most computationally expensive part of MD. Is it thus reasonable to say that MD overall scales as O(N logN)? Or does MD overall scale in some other way? I have been having difficulty finding a textbook or paper that states or estimates the scaling of MD. Thank you so much for your time! Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjcat set timestep/amb2gmx?
Hi, yes Marc you are right but the last time I used gromacs on a namd trajectory I noticed that time in the output files is useless 'cause it is always 0. I understand that, since this information is usually took from .trr or .xtc, it cannot be extracted from a .dcd, but it could be more useful using as x the frame number. This could, at least, permitting to visualize the plot with xmgrace without postprocessing the .xvg Francesco 2013/4/16 Mark Abraham mark.j.abra...@gmail.com On Apr 15, 2013 6:27 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/15/13 12:23 PM, Steven Neumann wrote: Dear Gmx Users, I obtained dcd trajectory from simulation in another software. I wish to merge many trajectories using trjcat with a proper timestep. Is that option possible using gromacs or shall use a script to produce tpr file from my prmtop file e.g. amb2gmx ? Any links for such a script? If you linked against VMD libraries when installing, Gromacs can handle any trajectory/coordinate file format that VMD can, thus requiring no conversion. If you need a .tpr file to do the analysis you are trying to do, then yes, you need to convert topology information into the proper format. ...and be aware that a -s option that accepts both .tpr and (say) .gro formats (as shown in g_tool -h) might succeed with the latter if only atom names, rather than (say) bonding connectivity is required for g_tool to work. Mark -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] replica exchange data in cpt file
This is what I meant, in particular it is a problem when I want to analyze the data regarding the exchange probability. Francesco 2013/4/4 João Henriques joao.henriques.32...@gmail.com So let me see if I understood what Francesco said correctly. Restarting a REMD job after hitting the cluster wall-time limit resets the information stored in the log files? Can someone shed some light on this subject? Best regards, João Henriques -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] replica exchange data in cpt file
if your -append option is activated (the default is yes), maybe Demux.pl reads the exchanging from the .log taking into account the time in the log and so you don't need to do anything. But I don't know how Demux.pl works :( Francesco 2013/4/4 João Henriques joao.henriques.32...@gmail.com That's terrible! I was just about to restart 2 hefty REMD simulations... Maybe I can move the original log files somewhere and combine them with the restart ones afterwards by using a script. It's just an idea, because I need to run Demux.pl on the final concatenated log file. Any other issues I should be aware of? Best regards, João Henriques On Thu, Apr 4, 2013 at 12:18 PM, francesco oteri francesco.ot...@gmail.comwrote: This is what I meant, in particular it is a problem when I want to analyze the data regarding the exchange probability. Francesco 2013/4/4 João Henriques joao.henriques.32...@gmail.com So let me see if I understood what Francesco said correctly. Restarting a REMD job after hitting the cluster wall-time limit resets the information stored in the log files? Can someone shed some light on this subject? Best regards, João Henriques -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- João Henriques -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] .top file from .tpr and .xtc
Hi, if you were able to obtain a simulation it means you had a valid .top file! In any case, gromacs recognises disulfide basing on the distance beween the SG atoms. In addition, the two chains are supposed to be in the same molecule. So, my advice is, remove all the TER from pdb (but the last one), leave the chain id and use pdb2gmx with the option -chainsep ter. The result is supposed to be a topology where your chain are grouped in a single molecule,making possible to create the bridge, and at the same time you keep the chain name for future analysis. Francesco 2013/3/19 shahid nayeem msnay...@gmail.com Hi To be more clear I have .xtc file for a disulfide linked complex of two chains. From this trajectory I can extract .xtc file for individual chains. But when I generate .top file from individual chain pdb I get one atom extra in .top file i.e. protonated SG of Cys which I dont need in order to make my .xtc and .top file compatible. Shahid On Tue, Mar 19, 2013 at 2:07 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/18/13 12:35 PM, shahid nayeem wrote: Hi Is it possible to write .top file from .xtc and .tpr using index.ndx so that .top is available for tailormade components of simulated protein. All topology information is in the .tpr, but not in .top format. You may be able to post-process the output of gmxdump to produce some hacked version, but that's just a bit of a hand-waving guess. I don't really understand what your objective is. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] .top file from .tpr and .xtc
Could you simply edit the file and removing the atom from [atoms] section ? grompp wil complain regarding the line containing interactions. But also these few lines can be removed. Otherwise, vmd has the TopoTools that write the .top topology of the loaded pdb. Unfortunately, this topologyes are not useful for carrying out MD because they lack parameters. In any case are good for analysis! Francesco 2013/3/19 shahid nayeem msnay...@gmail.com Thanks Francesco. But my problem is exactly opposite. I do have a .top file containing both chain linked by disulfide bridge. I ran the simulation. Now I have extracted .xtc file for each chain separately and I want the corresponding, separate .top file for each chain. when I separate the pdb and run the pdb2gmx I get one hydrogen on SG atom of Cys which is absent in .xtc file. So the .top file generated this way has one atom more as compared to .xtc file. shahid On Tue, Mar 19, 2013 at 1:07 PM, francesco oteri francesco.ot...@gmail.com wrote: Hi, if you were able to obtain a simulation it means you had a valid .top file! In any case, gromacs recognises disulfide basing on the distance beween the SG atoms. In addition, the two chains are supposed to be in the same molecule. So, my advice is, remove all the TER from pdb (but the last one), leave the chain id and use pdb2gmx with the option -chainsep ter. The result is supposed to be a topology where your chain are grouped in a single molecule,making possible to create the bridge, and at the same time you keep the chain name for future analysis. Francesco 2013/3/19 shahid nayeem msnay...@gmail.com Hi To be more clear I have .xtc file for a disulfide linked complex of two chains. From this trajectory I can extract .xtc file for individual chains. But when I generate .top file from individual chain pdb I get one atom extra in .top file i.e. protonated SG of Cys which I dont need in order to make my .xtc and .top file compatible. Shahid On Tue, Mar 19, 2013 at 2:07 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/18/13 12:35 PM, shahid nayeem wrote: Hi Is it possible to write .top file from .xtc and .tpr using index.ndx so that .top is available for tailormade components of simulated protein. All topology information is in the .tpr, but not in .top format. You may be able to post-process the output of gmxdump to produce some hacked version, but that's just a bit of a hand-waving guess. I don't really understand what your objective is. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org
Re: [gmx-users] .top file from .tpr and .xtc
If it works then you are right :) 2013/3/19 shahid nayeem msnay...@gmail.com I did it. Simply I changed the name of Cys which forms interchain dsiulfide bond to CYS2 in the separated pdb file and I used G43a1 forcefeild to run pdb2gmx. This gives a topology with same number of atom which is present in .xtc file. CYS2 is present .rtp file of G43a1 forcefeild probably to form interchain disulfide bond reading from specbond.dat. Am I right in generating such half disulfide bond topology. shahid On Tue, Mar 19, 2013 at 2:10 PM, francesco oteri francesco.ot...@gmail.com wrote: Could you simply edit the file and removing the atom from [atoms] section ? grompp wil complain regarding the line containing interactions. But also these few lines can be removed. Otherwise, vmd has the TopoTools that write the .top topology of the loaded pdb. Unfortunately, this topologyes are not useful for carrying out MD because they lack parameters. In any case are good for analysis! Francesco 2013/3/19 shahid nayeem msnay...@gmail.com Thanks Francesco. But my problem is exactly opposite. I do have a .top file containing both chain linked by disulfide bridge. I ran the simulation. Now I have extracted .xtc file for each chain separately and I want the corresponding, separate .top file for each chain. when I separate the pdb and run the pdb2gmx I get one hydrogen on SG atom of Cys which is absent in .xtc file. So the .top file generated this way has one atom more as compared to .xtc file. shahid On Tue, Mar 19, 2013 at 1:07 PM, francesco oteri francesco.ot...@gmail.com wrote: Hi, if you were able to obtain a simulation it means you had a valid .top file! In any case, gromacs recognises disulfide basing on the distance beween the SG atoms. In addition, the two chains are supposed to be in the same molecule. So, my advice is, remove all the TER from pdb (but the last one), leave the chain id and use pdb2gmx with the option -chainsep ter. The result is supposed to be a topology where your chain are grouped in a single molecule,making possible to create the bridge, and at the same time you keep the chain name for future analysis. Francesco 2013/3/19 shahid nayeem msnay...@gmail.com Hi To be more clear I have .xtc file for a disulfide linked complex of two chains. From this trajectory I can extract .xtc file for individual chains. But when I generate .top file from individual chain pdb I get one atom extra in .top file i.e. protonated SG of Cys which I dont need in order to make my .xtc and .top file compatible. Shahid On Tue, Mar 19, 2013 at 2:07 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/18/13 12:35 PM, shahid nayeem wrote: Hi Is it possible to write .top file from .xtc and .tpr using index.ndx so that .top is available for tailormade components of simulated protein. All topology information is in the .tpr, but not in .top format. You may be able to post-process the output of gmxdump to produce some hacked version, but that's just a bit of a hand-waving guess. I don't really understand what your objective is. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org
[gmx-users] replica exchange data in cpt file
Dear gromacs users, I ran a REMD on a HPC cluster equipped with a queue system. For this reason I carried out the simulation dividing it in chuncks. Because of this, each run started using the .cpt file from the previous one. The simulation ran fine, but I noticed that the informations regarding attempts and probabilities are not stored so in each .log the data restart from 0 like a new simulation. Have I done something wrong or is it a known (except to me) issue? Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to get pdb2gmx to use an arbitrarily located forcefield.ff directory?
Hi Chris, I don't know if thngs changed in gromacs 4.6.x, but I succesfully did what you are triying to do setting the two variable GMXLIB and GMXDATA at the same time. Francesco 2013/3/5 Christopher Neale chris.ne...@mail.utoronto.ca Hello, I have downloaded the charmm36.ff directory and would like to use it with pdb2gmx. Everything works fine if I put it in the current directory or the share/gromacs/top directory of the binary that I am using. However, I'd like to be able to put the charmm36.ff directory in an arbitrary place. I tried setting GMXLIB, no luck. I also tried setting GMXDATA and also, separately, creating a directory structure share/gromacs/top/charm36ff and then setting GMXDATA to share/ (which seems absurdly convoluted, but is implied that it should work by the description of GMXDATA here http://www.gromacs.org/Documentation/Terminology/Environment_Variablesand the text at the output of pdb2gmx: Fatal error: Could not find force field 'charmm36' in current directory, install tree or GMXDATA path. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I can get around this by making a link in the current directory and then using sed to change the directory structure in the resulting .top file, after which I can remove the link in the .top file. Thank you for any advice, Chris. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] clusterization in dihedral space
Thank you Mark and Justin, do you have any reference where this kind of clustering is explained? I mean, since i need a parameter representing the difference between two frames to build the matrix, what is the parameter I can use starting from the dihedrals? Francesco 2013/1/22 Mark Abraham mark.j.abra...@gmail.com On Mon, Jan 21, 2013 at 8:06 PM, francesco oteri francesco.ot...@gmail.comwrote: Thank you, but I don't see how performing cluster analysis with g_angle g_dih never did do any clustering. As Justin said, g_angle with a suitable index group likely does the job for you. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] clusterization in dihedral space
Thank you, but I don't see how performing cluster analysis with g_angle Francesco 2013/1/21 Justin Lemkul jalem...@vt.edu On 1/21/13 1:54 PM, francesco oteri wrote: Dear gromacs users, I am trying to run dihedral space clustering with g_dih, but I found that it gives me a lot of error like: Dihedral around 24,26 not found in topology. Using mult=3 Looking on the net, I found something alarming: g_dih is gromos specific! http://lists.gromacs.org/**pipermail/gmx-users/2006-**August/023230.htmlhttp://lists.gromacs.org/pipermail/gmx-users/2006-August/023230.html It is still true? Yes, and it is for this reason that g_dih has been removed from Gromacs. You can likely accomplish whatever you're trying to do with g_angle. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Convert .psf to .top
Hi, in vmd there is a package called topotools ( https://sites.google.com/site/akohlmey/software/topotools). This package has the magic command writegmxtop. Be carefull 'cause the created .top might miss some information (tipically angles and dihedrals) so I advice you to carefully check the .top file. Francesco 2012/12/26 Kieu Thu Nguyen kieuthu2...@gmail.com Dear All, Are there any method that can convert CHARMM PSF files to Gromacs topology files ? Thank for any help ! Best regards, KT -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: gold-S simulation
Dear fatemeh, in the topology file there is a section called [ bonds ] where the covalent bonds are listed. You should add you bonds there. But I think modifing specbonds.dat is easier because it allows pdb2gmx to do the dirty job :) Anyway, f you have to simulate bond breaking, you can use Morse potential whose parameters can directly derived by the armonic form. Morse potential doesn't allow the bond breaking but the overall effect is very close! I have to admit I never used but only read about Morse potential so I cannot do practic advices! Francesco 2012/12/17 Justin Lemkul jalem...@vt.edu On 12/17/12 4:01 PM, fatemeh ramezani wrote: Dear Justin According to papers, I expect gold atom interacts with the sulfur atom of amino acid cysteine covalently. But in last email you said in the case of protein-Au This will not be true to add these parameters in topology file. Then in which file should I add the parameters between gold and sulfur? What do you suggest? How do I define for the program that can be established between these two atoms covalent bond ? Bonds do not break and form in standard MD. For that, you need QM or QM/MM type calculations. If there should be a bond between Cys and Au, you need to write that into the topology or use the specbond.dat mechanism. pdb2gmx will not create bonds between Au and Cys otherwise. The other modifications you have made, as far as I can tell, are fine. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gold-S simulation
Hi fatemeh, thank you for the references. Regarding your problem, what does it means you don't see any interaction? Is it possible it is just a problem of the visualization software. To be sure, you could monitor the distance between any S atom and the Au atom to which it is supposed to be bound. If the distance is stable around the equilibrium value you can say that the interaction is still present Francesco 2012/12/16 fatemeh ramezani fr_...@yahoo.com hi thanks for your attention, all itp files are in OPLSAA forcefield folder that I attached it for you. Fatemeh Ramezani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gold-S simulation
Hi fatemeh, I am looking for prameters like yours, where have you took the parameters for gold and gold-aminoacid inteaction? Francesco 2012/12/16 Peter C. Lai p...@uab.edu Where is the .itp file for the system? On 2012-12-15 01:40:27PM -0800, fatemeh ramezani wrote: hi I'm simulating gold atom interaction with aminoacidcys. I have made gold-cys.pdb by hyperchem software: HETATM1 N CYS 1 0.000 1.335 0.000 HETATM2 CA CYS 1 -0.683 1.818 -1.183 HETATM3 C CYS 1 -0.705 3.339 -1.221 HETATM4 O CYS 1 -0.184 3.993 -0.319 HETATM5 CB CYS 1 -2.127 1.330 -1.221 HETATM6 SG CYS 1 -3.106 1.859 -2.649 HETATM8 AU AU 8 -2.833 0.428 -1.793 HETATM9 AU AU 9 -2.647 0.381 -2.869 HETATM 10 AU AU 10 -1.691 1.360 -3.093 HETATM 11 AU AU 11 -0.647 2.706 -2.135 HETATM 12 AU AU 12 -2.742 0.834 -0.456 HETATM 13 AU AU 13 -1.691 2.061 -0.043 HETATM 14 AU AU 14 -0.783 3.136 0.376 HETATM 15 AU AU 15 0.095 3.750 -1.068 HETATM 16 AU AU 16 -2.929 2.480 -2.204 HETATM 17 AU AU 17 -3.285 1.594 -3.328 HETATM 18 AU AU 18 -2.544 2.593 -3.763 HETATM 19 AU AU 19 -1.951 1.260 -2.303 CONECT12 CONECT01 CONECT2135 CONECT02 CONECT324 CONECT43 CONECT526 CONECT05 CONECT05 CONECT65 CONECT06 CONECT06 CONECT06 END I started simulation by this pdb file. I'm using OPLSAA force field and also I added gold parameter in ffnonbonded.itp : . . . ; Added by DvdS 05/2005 copied from GROMACS force field. SI SI 1428.08000 0.000A3.38550e-01 2.44704e+00 AU AU 79 196.9700 0.000 A0.29510e+00 22.1120e+00 [ nonbond_params ] AU AU 10.0e+00 0.0e+00 ; SC 08/2007: Special Au-N vdw to simulate chemical bond between gold-imidazole AU opls_511 13.07000e-01 3.96000e+00 ; SC 05/2008: special Au-C and Au-H to simulate pi-systems alkenes+benzene (and PHE) AU opls_142 13.21000e-1 2.65400e+00 AU opls_143 13.21000e-1 2.65400e+00 AU opls_144 12.67000e-1 1.66500e+00 AU opls_145 13.2e-1 2.54600e+00 AU opls_146 12.67000e-1 1.66500e+00 AU opls_150 13.21000e-1 2.65400e+00 ; +imidazole and His AU opls_506 13.21000e-1 2.54000e+00 AU opls_507 13.21000e-1 2.54000e+00 AU opls_508 13.21000e-1 2.54000e+00 ; +HisH AU opls_509 13.21000e-1 2.54000e+00 AU opls_510 13.21000e-1 2.54000e+00 ; +TYR AU opls_166 13.21000e-1 2.54000e+00 ; +TRP AU opls_500 13.21000e-1 2.54000e+00 AU opls_514 13.21000e-1 2.54000e+00 AU opls_501 13.21000e-1 2.54000e+00 AU opls_502 13.55000e-1 3.55000e+00 and I concidered AU-S as bonding connection and I added its parameter (bond stretch, dihedral and angle ) in ffbonded.itp file: [ bondtypes ] ; ij func b0 kb . . . AUSH 10.24000 165528.0 ; AUS 10.24000 165528.0 ; AUSG 10.24000 165528.0 ; . . . [ angletypes ] ; ijk func th0 cth . . . AU SG CB 1 109.00 46.34 AU SH CB 1 109.00 46.34 AU S CB 1 109.00 46.34 . . . [ dihedraltypes ] . . . #define improper_AU_S_CB_CA-180.0 1.2958 2 #define improper_AU_SH_CB_CA -180.0 1.2958 2 #define improper_AU_SG_CB_CA-180 1.2958 2 #define improper_AU_S_C_C 19 0.9196 2 #define improper_AU_SH_C_C19 0.9196 2 #define improper_AU_SG_C_C19 0.9196 2 . . . when I run my simulation I dont see any interaction or affinity between gold atom and S atom of cystein, while it is clear that gold shoud has interaction with sulfur. what is its reason? I'm completely confused. I tried anythings that I can but my system doesn't
Re: [gmx-users] g_sas : Total surface area
Hi Kavya, Can you better describe your system? As Mark suggested, could you supply some number? Francesco 2012/12/12 Mark Abraham mark.j.abra...@gmail.com On Wed, Dec 12, 2012 at 9:06 AM, Kavyashree M hmkv...@gmail.com wrote: Dear users, I was calculating solvent accessible surface area for a trajectory using g_sas. I used an index file with 3 sets (A, B, C) of mutually exclusive residues but summing up to 20 amino acids. Then using g_sas calculated sas for these 3 sets separately and whole protein separately for the same trajectory. I was expecting that the average value of Total surface area (protein) ~ Total surface area (A)+Total surface area (B)+Total surface area (C) But it is not so. Could anyone explain me why? Not without seeing any numbers. You're probably thinking that the surface area of A excludes the interfacial area to the other sets, but it doesn't. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error with MARTINI depending by the box size
Tanks to all for your advices, I am going to check all the different aspect you suggested and I will report the results as soon as possible. Francesco 2012/12/11 Tsjerk Wassenaar tsje...@gmail.com Hi, Visualization is the key. If you check the structure right after genbox, you should be able to notice something odd. Apparently genbox has a problem with martini water, which probably means there is a problem with monoatomic solvents. The problem has been noted before, b ut I'm a bit too lazy now to check whether it was here or on the martini forum. Using a small box with a single water molecule for filling will solve the problem. Cheers, Tsjerk On Tue, Dec 11, 2012 at 12:06 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Mon, Dec 10, 2012 at 11:54 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/10/12 5:45 PM, francesco oteri wrote: For Justin, I need this water for one simple reason: less then 20nm doesn't workAs I said before It seems you have identified the source of the problem, and it is independent of box size. I questioned the box size because it seemed rather random and you had not shown any data for box sizes less than 19 nm, so I was curious how you arrived at the need for 20 nm, more than double the size of your solute. It would be interesting to see if you could identify a minimum box size that does not require large numbers of solvent configurations to be stacked within the unit cell. The only reason I could see for what you're reporting is if neighboring solvent blocks somehow get crossed to produce overlap when they should simply be next to one another. The larger the box, the greater the probability that this happens. Yeah, that's probably it. The water box has many waters with x coordinates down at 0.000 and near 10.901, with an x size of 10.902. So different box sizes will randomly introduce unstable water configurations according to whether stuff is too close. This water box is probably not suited to the purpose - its box size might not include the half VDW radii outside the water coordinates needed to pack stably. Mark 2012/12/10 francesco oteri francesco.ot...@gmail.com Hi Mark, you are right respect the -vdwd 0.4: In MARTINI tutorials they suggest to use 0.21. Since I still got errors with this procedure, I decided to remove water manually through vmd. Looking carefully at the configurations, I found that the water molecule originating the error is exactly superimposed to an other molecule so I simply deleted it and the same error is reported for an other water molecule. Although I could scan all the pdb to detect all the superimposed water molecules, I believed genbox checked for this. Of course the original box does't contain superimposed molecules. It is highly unusual for genbox to produce overlapping waters, but per the help description, only solute-solvent overlaps are checked, not solvent-solvent, which would likely require enormous amounts of memory (and genbox already has memory issues). -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests
Re: [gmx-users] Error with MARTINI depending by the box size
Actually, since I copied and pasted the mail, there is an imprecision. When I use 20nm as box side lenght I don't get any error, everything goes fine. I actually tested different size between 19 and 20 nm and I found that the minimum size to avoid the error is 19.5nm. My system has an average size and, as stated by vmd, it size are X = 8.851199722290039 Y= 8.751200151443481 Z=9.385200214385986 So a box of 20nm, as well as 19nm, is large enough to accomodate the protein. Moreover, since I remove the water around the protein (that is already stabie because of the in vacuo minimization), the problem has to be in the bulk water! Francesco 2012/12/10 Justin Lemkul jalem...@vt.edu On 12/10/12 3:48 PM, francesco oteri wrote: Dear gromacs users, I am facing a very tricky problem in building a stable topology. In particular I am trying to use MARTINI force-field and I noticed that if I use a box whose the side size is smaller than 20nm, the minimization fails with this message: Reading file 01em.tpr, VERSION 4.6-beta1 (single precision) Starting 12 tMPI threads Using 12 MPI threads Making 2D domain decomposition 4 x 3 x 1 Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps = 2000 Step= 14, Dmax= 1.2e-06 nm, Epot= 4.42099e+18 Fmax= inf, atom= 39063 Energy minimization has stopped, but the forces havenot converged to the requested precision Fmax 1000 (whichmay not be possible for your system). It stoppedbecause the algorithm tried to make a new step whose sizewas too small, or there was no change in the energy sincelast step. Either way, we regard the minimization asconverged to within the available machine precision,given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, butthis is often not needed for preparing to run moleculardynamics. You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 4.4209897e+18 Maximum force = inf on atom 39063 Norm of force = inf With this information, you should be able to deduce the source of the problem. gcq#142: One Ripple At a Time (Bianca's Smut Shack) But, if I use a box bigger then 19.5nm the minimization, although with some LINCS warning, succeeded! These LINCS warnings will also give the same information as to where problems start. I found the problem with gromacs 4.5.5, 4.6beta1 and beta2. I am attaching the script (crea_topo.csh) I am using to build the topologies as well as all the input files you need to replicate the error. The different topologies have been obtained changing the value of the variable side in crea_topo.csh How many values you have tried? What is the minimum box size necessary to accommodate your system? This all seems like random failures from unstable configurations. As you can notice from the script, the structure is initially minimized in vacuo to remove problems due in the all atoms-coarse grained transformation and then it is solvated, Then, water molecules closer then 0.8nm to protein are rmoved through vmd. What was the outcome of the in vacuo minimization? Can you give me some clue on how to solve the problem, except changing the software?. http://www.gromacs.org/**Documentation/Terminology/** Blowing_Up#Diagnosing_an_**Unstable_Systemhttp://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error with MARTINI depending by the box size
Hi Mark, you are right respect the -vdwd 0.4: In MARTINI tutorials they suggest to use 0.21. Since I still got errors with this procedure, I decided to remove water manually through vmd. Looking carefully at the configurations, I found that the water molecule originating the error is exactly superimposed to an other molecule so I simply deleted it and the same error is reported for an other water molecule. Although I could scan all the pdb to detect all the superimposed water molecules, I believed genbox checked for this. Of course the original box does't contain superimposed molecules. Francesco 2012/12/10 Justin Lemkul jalem...@vt.edu On 12/10/12 5:15 PM, francesco oteri wrote: Actually, since I copied and pasted the mail, there is an imprecision. When I use 20nm as box side lenght I don't get any error, everything goes fine. I actually tested different size between 19 and 20 nm and I found that the minimum size to avoid the error is 19.5nm. My system has an average size and, as stated by vmd, it size are X = 8.851199722290039 Y= 8.751200151443481 Z=9.385200214385986 So a box of 20nm, as well as 19nm, is large enough to accomodate the protein. Those box sizes are vast overkill. Any reason why you need so much extra water? Moreover, since I remove the water around the protein (that is already stabie because of the in vacuo minimization), the problem has to be in the bulk water! As I said before, you should be able to identify the source of the problem by simple visualization based on what mdrun has told you. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error with MARTINI depending by the box size
For Justin, I need this water for one simple reason: less then 20nm doesn't workAs I said before 2012/12/10 francesco oteri francesco.ot...@gmail.com Hi Mark, you are right respect the -vdwd 0.4: In MARTINI tutorials they suggest to use 0.21. Since I still got errors with this procedure, I decided to remove water manually through vmd. Looking carefully at the configurations, I found that the water molecule originating the error is exactly superimposed to an other molecule so I simply deleted it and the same error is reported for an other water molecule. Although I could scan all the pdb to detect all the superimposed water molecules, I believed genbox checked for this. Of course the original box does't contain superimposed molecules. Francesco 2012/12/10 Justin Lemkul jalem...@vt.edu On 12/10/12 5:15 PM, francesco oteri wrote: Actually, since I copied and pasted the mail, there is an imprecision. When I use 20nm as box side lenght I don't get any error, everything goes fine. I actually tested different size between 19 and 20 nm and I found that the minimum size to avoid the error is 19.5nm. My system has an average size and, as stated by vmd, it size are X = 8.851199722290039 Y= 8.751200151443481 Z=9.385200214385986 So a box of 20nm, as well as 19nm, is large enough to accomodate the protein. Those box sizes are vast overkill. Any reason why you need so much extra water? Moreover, since I remove the water around the protein (that is already stabie because of the in vacuo minimization), the problem has to be in the bulk water! As I said before, you should be able to identify the source of the problem by simple visualization based on what mdrun has told you. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] top2psf with Amber99SB-ILDN
hi,it would be nice knowing the errors. Francesco 2012/11/22, Steven Neumann s.neuman...@gmail.com: Dear Gmx Users, Is it possible to convert topology produced by Gmx and convert it ont the psf file? I used Justin script but when I load pdb and psf in VMD then there are some errors. Would you help? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] top2psf with Amber99SB-ILDN
yes,actually it works fine as long as you have one chain in you .top file . if u have more subunits, u are supposed to merge the chains using the appropriate value for -chainsep option in pdb2gmx 2012/11/22, Steven Neumann s.neuman...@gmail.com: There was an error with index 1 which this script assigned to bond part. The script provided here: http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/top2psf/top2psf.pl works much better. Steven On Thu, Nov 22, 2012 at 12:50 PM, francesco oteri francesco.ot...@gmail.com wrote: hi,it would be nice knowing the errors. Francesco 2012/11/22, Steven Neumann s.neuman...@gmail.com: Dear Gmx Users, Is it possible to convert topology produced by Gmx and convert it ont the psf file? I used Justin script but when I load pdb and psf in VMD then there are some errors. Would you help? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: hydrophobic contacts
Hi, if you don't want to be very accurate, you can select basing on the residue name since LEU, ILE, VAL...etc, are universally considered hydrophobic 2012/11/14 Justin Lemkul jalem...@vt.edu On 11/14/12 2:27 AM, Raj wrote: Hi all, can some one tel me how can i prepare a index file specifying the hydrophobic atoms along for measuring the hydrophobic contacts in the systems alone. There is no straightforward way to do this, as far as I know. I generally construct such groups by selecting groups of hydrophobic residues and then parse out the hydrophobic atoms within these groups. You can narrow down your selections using default groups like Sidechain (since the protein backbone is highly polar) and select by atom type using a .tpr file as the input to make_ndx. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Continuous mdrun vs step-by-step mdrun
Hi, happy diwali to you, too. Can you please post a link where what you said is stated? it seems quite strange to me! 2012/11/12 Venkat Reddy venkat...@gmail.com Dear gromacs users, I have a very basic doubt regarding mdrun. Is there any difference between doing final MD for 100 ns at a stretch and doing the same with a 10 ns step size (*i.e., 10ns20ns30ns100ns*) on a cluster of 256 processors. I have read some where that continuous MD of longer simulations will cause spurious drifts in velocity and energy, errors in velocity correlationetc. Please advise me in this regard. Thank you and Happy DIWALI -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] PCA
Hi Tuba, I guess you have to create an index for each peptide and then extracting covariance matrix on each peptide using the new indexes. Francesco 2012/11/6 Tuba Kilinc tkil...@gmail.com hi all, i would like to apply PCA (principal component analysis) for my peptides that i simulated. i do know PCA for one trajectory but what if i have more than one peptide ? how can i apply pca for example 10 peptides in a box ? typically, i start with a PCA on the simulation with g_covar -s protein.pdb -f traj.xtc -v eigenvec.trr and i create projections on PCA vectors using g_anaeig i have to extract a trajectory for each peptide and concatenate those trajectories and i need to make an index group for each peptide in each system that i include but i couldnt figure out extract a trajectory for each group for each system? Could you help me please ? thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Martini FF for Sec structure changes...
Hi rama, actually MARTINI has been further improved to allow secondary structure change. The title is: *Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides* and here there is a link to the paper: http://dx.doi.org/10.1021/ct200876v Francesco 2012/10/10 XAvier Periole x.peri...@rug.nl Nope, but on other softwares. On Oct 10, 2012, at 2:50 PM, rama david wrote: Thank you for your reply, Are these Cg can be used in Gromacs. Thank you in advance. With best wishes and regards, Rama david On Wed, Oct 10, 2012 at 6:13 PM, XAvier Periole x.peri...@rug.nl wrote: Martini FF cannot model changes in secondary structure ... other CG FF can. You'll find them easily in the literature. Notably the ones from Deserno or Derreumaux. On Oct 10, 2012, at 2:03 PM, rama david wrote: Hi friends, I planed to use the martini force-field for my simulation study of peptide. The peptides are initially alpha-helix in nature. As they come together they formed amyloid fibre( Antiparallel Beta structure). Is it is possible to study the secondary structure backbone study by martini force field. I read in there tutorial that the Secondary structure is predefined therefore they are statics through out the simulation. Conformational changes that produces changes in Sec structure are out of scope in martini. only tertiary structure are free defined to change.. So what to do ??? How to use Martini FF to study secondary structure ??? Is there any way to use coarse grained FF to use for study in Sec. structure??? With Best wishes and regards, Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Interaction study for peptide-receptor..
Hi, as far as I know, freezing just set velocities to 0 so you gain nothing freezing atoms. By the way, have you tried docking? It takes into account multiple conformation and orientation of the peptide and, depending upon the implemented algorithm, also protein sidechain orientation. Francesco 2012/10/4 rama david ramadavidgr...@gmail.com thank you Justin for reply. I dont know about long range interactions. But as I freeze the group I think it will improve my computational speed. So is there any way to find out or decide which group should be freeze, and which group should affect my interaction most probably?? Should I do Essential Dynamics ??? or Principle component analysis ??? Would you suggest me any general protocol for such work?? Thank you in Advance With Best Wishes and regards. Rama David On Thu, Oct 4, 2012 at 3:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/4/12 2:01 AM, rama david wrote: Hi gromacs Friends, I want to do peptide-receptor ( Protein) interaction study.Receptor consist a single chain. Peptide is made up of 4 amino acids. I know the interaction pattern of peptide and receptor. I plan to mutate single residue each at a time and run 4 simulation . So I will have the 4 different simulation that contain the mutated residues and the wild one. Then afterward from the interaction energy I want to select the peptide which is showing stronger interaction than others. As mention I know the binding site, If I freeze the remaining portion in receptor that not involved in binding , Is it going to affect my screening process ??? Potentially. Do you know that the binding interactions and the mutations will only perturb local residues? Do you know that there are no long-range motions to be considered? I think you gain very little by freezing portions of the system, and risk more than you gain. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Interaction study for peptide-receptor..
2012/10/4 rama david ramadavidgr...@gmail.com Hi francesco, Thank you For reply. I did docking but the result are not so impressive. What does it mean not so impressive? I mean, do you have experimental data and the comparison with docking doesn't agree with experiments? Have you generated a sufficient number of complexes (say 100 or more)? I used vina and autodock. I also did virtual screening in autodock but the result are not upto the mark. Is the freezing of group can affect my system?? How much efficiency I get by these work?? It will change a lot the dynamics of your system and I don't think calculations will be more efficient! As these group are going to freeze in four simulation so if it affect one ligand it affect other ligand also. I read article that did the work like me , they sliced the binding residues and used the inert solid sphere to support binding residues instead of the freezing group other group. I think both way should have same effect..Am I right or wrong?? If you have any other way please suggest it.. If you already have docking complexes, you can pick up one complex for each peptide, to run an MD, or Free Energy calculations. It strongly depends by the experimentale data you have and what is the target of your work. With best wishes and regards Rama david On Thu, Oct 4, 2012 at 5:07 PM, francesco oteri francesco.ot...@gmail.comwrote: Hi, as far as I know, freezing just set velocities to 0 so you gain nothing freezing atoms. By the way, have you tried docking? It takes into account multiple conformation and orientation of the peptide and, depending upon the implemented algorithm, also protein sidechain orientation. Francesco 2012/10/4 rama david ramadavidgr...@gmail.com thank you Justin for reply. I dont know about long range interactions. But as I freeze the group I think it will improve my computational speed. So is there any way to find out or decide which group should be freeze, and which group should affect my interaction most probably?? Should I do Essential Dynamics ??? or Principle component analysis ??? Would you suggest me any general protocol for such work?? Thank you in Advance With Best Wishes and regards. Rama David On Thu, Oct 4, 2012 at 3:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/4/12 2:01 AM, rama david wrote: Hi gromacs Friends, I want to do peptide-receptor ( Protein) interaction study.Receptor consist a single chain. Peptide is made up of 4 amino acids. I know the interaction pattern of peptide and receptor. I plan to mutate single residue each at a time and run 4 simulation . So I will have the 4 different simulation that contain the mutated residues and the wild one. Then afterward from the interaction energy I want to select the peptide which is showing stronger interaction than others. As mention I know the binding site, If I freeze the remaining portion in receptor that not involved in binding , Is it going to affect my screening process ??? Potentially. Do you know that the binding interactions and the mutations will only perturb local residues? Do you know that there are no long-range motions to be considered? I think you gain very little by freezing portions of the system, and risk more than you gain. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users
Re: [gmx-users] Regarding g_cluster process MPI enabled
Hi... you have to implement the algorithm using parallel paradigma (MPI, openmp, thread) Alternatively, there is a workaround to bypass the serial rmsd matrix building (the most time consuming part). g_cluster reads a rmsd matrix as input, you can run different rmsd instance in parallel, using appropriate input, in order to obtain the different rows of the matrix. Next, you have to collect these outputs through in order to have the .xpm file through an appropriate script (that you have to write). This matrix can be used as input to g_cluster that will use it to calculate clusters Francesco 2012/10/2 R.Vidya Rajendran (10PHD013) vidya2...@vit.ac.in Dear Friends, Gromacs script such as g_cluster takes lot of time to complete in a single machine. Is their any way to give this job to a cluster machine like mdrun. Since mdrun is MPI enabled so I can easily execute it on cluster. Anybody in group have any clue that how we can execute g_cluster command on a cluster machine ? regards Vidya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] why the output of g_saltbr is so large?
Hi, because g_saltbr calculates the data regarding any charge-charge interaction ( neg neg, neg pos, pos pos). Small problem: every atoms (C,H,S,P...) has a charge so the outputs contains the distances among al the n*(n-1)/2 atom couples Francesco 2012/9/21 Albert mailmd2...@gmail.com Dear: I am using command: g_saltbr -f md.trr -s tuned.tpr -dt 16800 to calculate the saltbr and I found the output is really large: ls -lt *.xvg -rw-r--r-- 1 albert users 640869568 Sep 21 09:53 min-min.xvg -rw-r--r-- 1 albert users 2392154038 Sep 21 09:53 plus-min.xvg -rw-r--r-- 1 albert users 2205434558 Sep 21 09:53 plus-plus.xvg could someone tell me how to make the output to be smaller? thank you very much best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Analysis of enssemble of MD trajectories
Hi, 2012/9/21 James Starlight jmsstarli...@gmail.com Dear collegues Thank for advices. Indeed Gromacs is able to analyse two trajectories with g_rms ( with the flags -f and -f2 ) but as the result I've obtain graph with one rmsd plot so I'm not sure about implementation of that method. In this case it computes the n1*n2 rmsd matrix! Each frame of the first trajectory is compared with the second trajectory. So I think that the algorithm proposed by Justin was exactly what I need. But I'm not sure also how I could do such ploating of results of the different g_rms analyses to one common graph ( when I analyse new trajectory and save it by the -o result.xvg if the result.xvg was already exist the old graph is back up to the #result.xvg# etc ). James 2012/9/20 lloyd riggs lloyd.ri...@gmx.ch: Dear Dr. I might be wrong, but I think you can use g_rms with two seperate trj files, and it takes the rms from the starting structure of the first one. In which case you would have to decide which is the reference, and then just do it three times. Theres also auxiliarry software which has plugins for this, such as VMD, Pymol, or even O run in some sort of batch. In pymol I know it can be run as a script, but you need all saved pdb files extracted from each trj, so would be a bit large and pain. with the VMD it has plugins for them, but I only played with it once. If you only want to look at beginning and end rms from say the start and end for all traj-using just a couple pdb at either end would be easy in pymol and O. There is also these new tools I found in Bio R (its called Bio3D if you look on the web for the freeware) , which are all scripts that I tried once, which work as well, mostly the take a reference structure and parse the pdbs output from a trj (if you write out each individually) but there values are different but directtly correlatable (ie say 1.6 from the former and something like 80% is cranked out by the later Vs 0.4 and 5% meaning no change) Hope that helps, and if I am wrong about something somone corrects me. Stephan Watkins Original-Nachricht Datum: Thu, 20 Sep 2012 14:06:40 +0400 Von: James Starlight jmsstarli...@gmail.com An: Discussion list for GROMACS users gmx-users@gromacs.org Betreff: [gmx-users] Analysis of enssemble of MD trajectories Dear Gromacs Users! I'm working with the enssemble of the MD trajectories calculated for the common protein with the differences in the initial conditions in the case of each trajectory. Now I'd like to perform analysis of that enssemble of data. For example I'de like to obtain RMSD as well as RMSF graphs calculated from all trajectories in one common graph for comparison of the dynamics of the systems. I've used trjcat on my 4 trajectories to obtain one merged trajectory multi.xtc and than tried to calculate RMSD for that multi.xtc but the resulted graph was wrong. trjcat -f md_150ns.xtc md_320ns.xtc sd_125.xtc sd_75ns.xtc -cat -tu ps -o multi.xtc Is there any other way to do such analysis of several trajectories in common graph? James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Photodissociation through MD
Hi, could you try to use the Morse potential for this bond. As far as I know, the parameters can be directly obatined forml the armonic potential expression. Francesco 2012/9/21 Mark Abraham mark.abra...@anu.edu.au On 21/09/2012 11:35 AM, Rajiv Gandhi wrote: Dear all gromacs users, In myoglobin system, how we can cut the bond between Fe-C to produce the photodissociation through MD?. By not making it in your topology. Whatever procedure you follow for making the other Fe-C interactions needs to differ from the one you wish to model the cleaved bond. Mark I have seen there are number of studies over photodissociation and also I believe that people have used their appropriate parameterization files to cut these bond. I am struct with this parameter and cutting bond process. It would be really appreciated if anyone can give some suggestion/information about this. Thanks a lot. Sincerely Rajiv -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] why the output of g_saltbr is so large?
You should modify g_saltbr code. Alternativley, you can create a fake .top file where charge are 0 except on carged groups (i.e. carboxylic atoms) that are supposed to interact. This new .top file can be used to have a new .tpr where only the interesting atoms are charged and are detected by g_saltbr as part of a putative interaction. Francesco 2012/9/21 Albert mailmd2...@gmail.com On 09/21/2012 10:48 AM, francesco oteri wrote: Hi, because g_saltbr calculates the data regarding any charge-charge interaction ( neg neg, neg pos, pos pos). Small problem: every atoms (C,H,S,P...) has a charge so the outputs contains the distances among al the n*(n-1)/2 atom couples Francesco Hello : thank you very much for kind reply. Is it possible simple restrict the calculation to protein sidechain? thank you very much best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] is NOASSEMBLYLOOPS broken?
Dear gromacs users (and eventually developers too),
I am trying to debug gromacs and on the gromacs website
http://www.gromacs.org/Developer_Zone/Programming_Guide/Programmer's_Guide#local_index
It is stated:
gromacs can be forced to use non assembly routines to do force
calculations (easier to debug) by defining NOASSEMBLYLOOPS=1 as
environment variable (e.g. put export NOASSEMBLYLOOPS=1 without the
quotes in your /etc/profile)
I tried to use this approach, but it doesn't work since gdb goes
inside the assembly loop.
Moreover, in order to check spelling errors I got each getenv call:
grep -R getenv `find -name *.c`
./src/kernel/fflibutil.c:lib = getenv(GMXLIB);
./src/kernel/runner.c:if ((env = getenv(GMX_MAX_THREADS)) != NULL)
./src/kernel/runner.c:
getenv(GMXGHAT),inputrec, (Flags MD_REPRODUCIBLE));
./src/kernel/readir.c: if (getenv(GALACTIC_DYNAMICS) == NULL) {
./src/kernel/pdb2gmx.c:bFFRTPTERRNM =
(getenv(GMX_NO_FFRTP_TER_RENAME) == NULL);
./src/kernel/do_gct.c:if ((buf = getenv(DISTGCT)) == NULL)
./src/kernel/md.c:if (getenv(GMX_FORCE_UPDATE))
./src/ngmx/logo.c: if ((newcol=getenv(LOGO))!=NULL)
./src/ngmx/x11.c: fontname=getenv(GMXFONT);
./src/ngmx/x11.c: display=getenv(DISPLAY);
./src/contrib/do_multiprot.c:if ((mptr=getenv(MULTIPROT)) == NULL) {
./src/contrib/do_shift.c: if ((dptr=getenv(TOTAL)) == NULL)
./src/gmxlib/tpxio.c:env = getenv(GMX_NOCHARGEGROUPS);
./src/gmxlib/checkpoint.c:if
(getenv(GMX_IGNORE_FSYNC_FAILURE_ENV)==NULL)
./src/gmxlib/checkpoint.c:if
(getenv(GMX_ALLOW_CPT_MISMATCH) == NULL)
./src/gmxlib/statutil.c:select = getenv(GMXTIMEUNIT);
./src/gmxlib/statutil.c:select = getenv(GMX_VIEW_XVG);
./src/gmxlib/statutil.c:envstr = getenv(GMXNPRIALL);
./src/gmxlib/statutil.c:envstr = getenv(GMXNPRI);
./src/gmxlib/mtop_util.c:env = getenv(GMX_MAXRESRENUM);
./src/gmxlib/disre.c:ptr = getenv(GMX_DISRE_ENSEMBLE_SIZE);
./src/gmxlib/viewit.c:if (getenv(DISPLAY) == NULL) {
./src/gmxlib/viewit.c: if ( ! (cmd=getenv(env)) ) {
./src/gmxlib/viewit.c:if ( getenv(XMGR) )
./src/gmxlib/viewit.c: if ( ! (cmd=getenv(env)) )
./src/gmxlib/enxio.c:if (getenv(GMX_ENX_NO_FATAL) != NULL)
./src/gmxlib/main.c:if (getenv(GMX_CHECK_MPI_ENV) == NULL)
./src/gmxlib/network.c: if (getenv(GMX_NO_NODECOMM) == NULL) {
./src/gmxlib/gmx_fatal.c:if ((temp=getenv(WHERE)) != NULL)
./src/gmxlib/futil.c:env = getenv(GMX_MAXBACKUP);
./src/gmxlib/futil.c:if (bUnbuffered ||
((bufsize=getenv(LOG_BUFS)) != NULL)) {
./src/gmxlib/futil.c:if (!found (s=getenv(PATH)) != NULL)
./src/gmxlib/futil.c:lib=getenv(GMXLIB);
./src/gmxlib/copyrite.c: return (getenv(GMX_NO_QUOTES) == NULL);
./src/gmxlib/vmdio.c:pathenv = getenv(VMD_PLUGIN_PATH);
./src/gmxlib/txtdump.c: if (getenv(LONGFORMAT) != NULL)
./src/gmxlib/sighandler.c:if (getenv(GMX_NO_TERM) == NULL)
./src/gmxlib/sighandler.c:if (getenv(GMX_NO_INT) == NULL)
./src/gmxlib/sighandler.c:if (getenv(GMX_NO_USR1) == NULL)
./src/gmxlib/nonbonded/nonbonded.c:
if(getenv(GMX_NOOPTIMIZEDKERNELS) != NULL)
./src/mdlib/shellfc.c: shfc-bPredict = (getenv(GMX_NOPREDICT) == NULL);
./src/mdlib/shellfc.c:shfc-bForceInit = (getenv(GMX_FORCEINIT) != NULL);
./src/mdlib/qm_orca.c: buf = getenv(BASENAME);
./src/mdlib/qm_orca.c: buf = getenv(ORCA_PATH);
./src/mdlib/ns.c: fr-ns.bCGlist = (getenv(GMX_NBLISTCG) != 0);
./src/mdlib/ns.c:char *ptr=getenv(GMX_DUMP_NL);
./src/mdlib/tpi.c:ptr = getenv(GMX_TPIC_MASSES);
./src/mdlib/tpi.c: dump_pdb = getenv(GMX_TPI_DUMP);
./src/mdlib/forcerec.c:if (getenv(GMX_NO_SOLV_OPT))
./src/mdlib/forcerec.c: getenv(GMX_NO_ALLVSALL) == NULL
./src/mdlib/forcerec.c:env = getenv(GMX_SCSIGMA_MIN);
./src/mdlib/forcerec.c:if (getenv(GMX_NB_GENERIC) != NULL)
./src/mdlib/forcerec.c:fr-UseOptimizedKernels =
(getenv(GMX_NOOPTIMIZEDKERNELS) == NULL);
./src/mdlib/forcerec.c:if (getenv(GMX_FORCE_TABLES))
./src/mdlib/qm_gaussian.c:buf = getenv(NCPUS);
./src/mdlib/qm_gaussian.c:buf = getenv(MEM);
./src/mdlib/qm_gaussian.c:buf = getenv(ACC);
./src/mdlib/qm_gaussian.c:buf = getenv(CPMCSCF);
./src/mdlib/qm_gaussian.c:buf = getenv(SASTEP);
./src/mdlib/qm_gaussian.c:buf = getenv(GAUSS_DIR);
./src/mdlib/qm_gaussian.c:buf = getenv(GAUSS_EXE);
./src/mdlib/qm_gaussian.c:buf = getenv(DEVEL_DIR);
./src/mdlib/qm_gaussian.c: * environment using getenv().
./src/mdlib/qm_gaussian.c:buf = getenv(STATE);
./src/mdlib/constr.c: char *env=getenv(GMX_SUPPRESS_DUMP);
./src/mdlib/constr.c:env = getenv(GMX_MAXCONSTRWARN);
./src/mdlib/gmx_wallcycle.c:if (PAR(cr)
getenv(GMX_CYCLE_BARRIER) != NULL)
./src/mdlib/gmx_wallcycle.c:if (getenv(GMX_CYCLE_ALL) != NULL)
./src/mdlib/nsgrid.c:ptr = getenv(GMX_NSCELL_NCG);
./src/mdlib/mdebin.c:md-bConstrVir =
(getenv(GMX_CONSTRAINTVIR) != NULL);
./src/mdlib/mdebin.c:md-bEner[i] =
Re: [gmx-users] 1replica/1cpu problem
Sorry for the multiple emails but everytime I tried to send the mail I obtained a message like this: The message's content type was not explicitly allowed. Please send your messages as plain text only. See http://www.gromacs.org/Support/Mailing_Lists; So I tried as long as no message has been replied to me. Concerning the bug fixes, I did the following steps git clone git://git.gromacs.org/gromacs.git gromacs-4.5.5-patches cd gromacs-4.5.5-patches git checkout --track -b release-4-5-patches origin/release-4-5-patches git pull ./bootstrap ./configure --prefix=/ibpc/etna/oteri/PKG/gromacs/4.5.5/patched --without-x --enable-mpi --program-suffix=_mpi --enable-all-static CFLAGS=-I/ibpc/etna/oteri/PKG/openmpi/1.4.5/include -I/ibpc/etna/oteri/PKG/fftw/3.3.1/gcc/include LDFLAGS=-L/ibpc/etna/oteri/PKG/fftw/3.3.1/gcc/lib -L/ibpc/etna/oteri/PKG/openmpi/1.4.5/lib LIBSUFFIX=_mpi make mdrun make install-mdrun 2012/7/19 Mark Abraham mark.abra...@anu.edu.au: On 19/07/2012 12:32 AM, francesco oteri wrote: Dear gromacs users, I am trying to run a replica exchange simulation using the files you find in http://dl.dropbox.com /u/40545409/gmx_mailinglist/inputs.tgz The 4 replicas have been generated, as following: grompp -p rest2.top -c 03md.gro -n index.ndx -o rest2_0 -f rest2_0.mdp grompp -p rest2.top -c 03md.gro -n index.ndx -o rest2_1 -f rest2_1.mdp grompp -p rest2.top -c 03md.gro -n index.ndx -o rest2_2 -f rest2_2.mdp grompp -p rest2.top -c 03md.gro -n index.ndx -o rest2_3 -f rest2_3.mdp The simulation was started with command, using gromacs 4.5.5 with the latest bug fix: Which bug fix? How did you apply it? Mark mpirun -np 4 mdrun_mpi -s rest2_.tpr -multi 4 -replex 1000 out1 giving the following error: [etna:10799] *** An error occurred in MPI_comm_size [etna:10799] *** on communicator MPI_COMM_WORLD [etna:10799] *** MPI_ERR_COMM: invalid communicator [etna:10799] *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort) -- mpirun has exited due to process rank 0 with PID 10796 on node etna exiting without calling finalize. This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -- [etna:10795] 3 more processes have sent help message help-mpi-errors.txt / mpi_errors_are_fatal [etna:10795] Set MCA parameter orte_base_help_aggregate to 0 to see all help / error messages The nice thing is that the same error doesn't appear either if I use the 4.5.5 without applying tha patches!!! mpirun -np 4 mdrun_mpi -s rest2_.tpr -multi 4 -replex 1000 out2 or the bug fixed with multiple processors per replica: mpirun -np 8 mdrun_mpi -s rest2_.tpr -multi 4 -replex 1000 out3 Since I have to use more then 4 replicas, I need to run 1cpu/replica. Has someone any idea of the probem? Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] 1replica/1cpu problem
Dear gromacs users, I am trying to run a replica exchange simulation using the files you find in http://dl.dropbox.com /u/40545409/gmx_mailinglist/inputs.tgz The 4 replicas have been generated, as following: grompp -p rest2.top -c 03md.gro -n index.ndx -o rest2_0 -f rest2_0.mdp grompp -p rest2.top -c 03md.gro -n index.ndx -o rest2_1 -f rest2_1.mdp grompp -p rest2.top -c 03md.gro -n index.ndx -o rest2_2 -f rest2_2.mdp grompp -p rest2.top -c 03md.gro -n index.ndx -o rest2_3 -f rest2_3.mdp The simulation was started with command, using gromacs 4.5.5 with the latest bug fix: mpirun -np 4 mdrun_mpi -s rest2_.tpr -multi 4 -replex 1000 out1 giving the following error: [etna:10799] *** An error occurred in MPI_comm_size [etna:10799] *** on communicator MPI_COMM_WORLD [etna:10799] *** MPI_ERR_COMM: invalid communicator [etna:10799] *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort) -- mpirun has exited due to process rank 0 with PID 10796 on node etna exiting without calling finalize. This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -- [etna:10795] 3 more processes have sent help message help-mpi-errors.txt / mpi_errors_are_fatal [etna:10795] Set MCA parameter orte_base_help_aggregate to 0 to see all help / error messages The nice thing is that the same error doesn't appear either if I use the 4.5.5 without applying tha patches!!! mpirun -np 4 mdrun_mpi -s rest2_.tpr -multi 4 -replex 1000 out2 or the bug fixed with multiple processors per replica: mpirun -np 8 mdrun_mpi -s rest2_.tpr -multi 4 -replex 1000 out3 Since I have to use more then 4 replicas, I need to run 1cpu/replica. Has someone any idea of the probem? Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] CMAP and Free Energy
Dear gromacs developers, is there any plan to make the CMAP correction avalaible for Free Energy Calculations? Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] floating point exception in .xtc file
Hi Christopher, you can try to use the program gmx_rescue, by Marc Baaden to recovery your trajectory. Below there is the adderess: http://baaden.free.fr/soft/compchem.html Francesco 2012/6/9 Mark Abraham mark.abra...@anu.edu.au On 9/06/2012 7:27 AM, Christopher Neale wrote: Dear Users: I have a 500 ns trajectory of 65 GB that gives a floating point exception when I run it through gmxcheck or trjcat (generated and analyzed with gromacs 4.5.5). Has anybody encountered this? I ran mdrun with -append so this is the xtc resulting from months of simulation of a 1,000,000 atom system. If I run trjconv -f md.xtc -b 20, where the floating point exception occurred around t=18 ps in gmxcheck, then I can extract the readable frames and repair around the damaged section. Still, I'd rather not lose any data and I had thought that the new default -append option to mdrun checked for these types of problems at runtime. I've no idea what might happen when some file-system transient occurs mid-simulation, but if mdrun has managed to compute a checksum on an incomplete file and stored that in the checkpoint, then the append mechanism can be none the wiser. The check upon restart is that the checksum matches, not that the checksum is computed on a file whose properties would satisfy gmxcheck. Note also that some file systems that do not support file locking and this is known to cause issues (Redmine 924), but I don't know if this is related to your observation. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Writing and compiling new analyses for gromacs
Dear Peter, usually I use a simple Makefile like # Variables set by the configuration script: GMX_HOME = /home/oteri/PKG/gromacs/4.5.5/gcc/ GMX_SRC = /home/oteri/PKG/sources/gromacs-4.5.5 GSL_HOME = /home/oteri/PKG//gsl/1.15/gcc MOD_HOME = /home/oteri/PKG/utilities/src MOD_BIN = /home/oteri/PKG/utilities/bin LIBS = -lgmxana -lmd -lgmx -lgsl -lnsl -lm -lSM -lICE -lpthread -lgslcblas LDFLAGS = -L$(GMX_HOME)/lib -L$(GSL_HOME)/lib $(LIBS) INCLUDE =-I/usr/X11R6/include -I/usr/include/libxml2 -I $(GSL_HOME)/include -I$(GMX_HOME)/include -I$(GMX_HOME)/include/gromacs -I$(GMX_SRC)/src/tools #-DDEBUG CFLAGSD = -O3 -fomit-frame-pointer -finline-functions -Wno-unused -funroll-all-loops -std=gnu99 $(INCLUDE) CFLAGS = -O0 -std=gnu99 -ggdb -O0 $(INCLUDE) CC = gcc LD = $(CC) # The real make targets - note that most make programs support # the shortcut $^ instead of listing all object files a second # time, but we cannot count on it... all: gmx_whatever gmx_whatever: gmx_whatever.o $(LD) $(CFLAGS) $(LDFLAGS) -o $(MOD_BIN)/$@ $(@).o $(LIBS) And it works fine! Regardiing the common function used, the only help I found is the gromacs source code. There are functions to read/write topology, frames, odb/gro file and so on Francesco 2012/6/4 Peter C. Lai p...@uab.edu On 2012-06-04 05:23:10PM -0400, Justin A. Lemkul wrote: On 6/4/12 5:16 PM, Shay Teaching wrote: 2012/6/4 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu On 6/4/12 2:59 PM, Shay Teaching wrote: Dear Gromacs users, I want to write new analyses for gromacs and compile it (so I'll have g_whatever) as part of the gromacs package. Per the instructions I found on gromacs website, I installed kdevelop and opened the gromacs as a project using kdevelop. However I have two questions: 1) When I try to compile gromacs source, through kdevelop, I get a permission denied error. I think it is because gromacs installation requires root privileges. Any suggestions on how to bypass that, so I won't have to use kdevelop as root (which is a *really* bad idea)? (e.g., installing gromacs without root?) Assuming you're trying to compile template.c in some system-level directory, you're certain to run into that problem. Compile in a different location. Actually, I tried installing Gromacs to my home directory, not system directory. You're saying that I'm not supposed to encounter this error? You shouldn't have permission errors in your home directory. I've never used KDevelop; what happens if you try to compile from a normal command line? My guess is that KDevelop isn't re-running configure and/or ccmake to set PREFIX correctly before make. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] hydration layers around protein
nice suggestioncoletta for ever PS. Lo so che è un commento inutile, ma qualcosa la devo pur dire :D 2012/5/29 Andrea Coletta andrea.cole...@uniroma2.it One option is to calculate the rdf (radial distribution function g_rdf [-surf]) of water oxygen atoms and find the position of the first few peaks... Il 29/05/2012 12:28, Bala subramanian ha scritto: Friends, I read in many articles explaining the behaviour of water in the first (or second etc) hydration layers around a protein. I am curious to know if there is any way to obtain/guess the thickness of this layer. How does one defines the thickness ? Thanks, Bala -- C. Balasubramanian -- *** Andrea Coletta - PhD Dip.to di Biologia - Stanza 326 Facoltà di Scienze - Università degli Studi di Roma Tor Vergata Via della Ricerca Scientifica snc, 00133, Roma, Italia Tel. +390672594326 Fax +39062022798 E-Mail: andrea.coletta_at_uniroma2_dot_it *** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] multiple dihedral definition and free energy calculation
Dear gromacs users, I am trying to run free energy calculation using the CHARMM force-field. I am able to generate the .top file, but when I try to obtain the .tpr, grompp gives the following error: ERROR 1 [file rest2.top, line 11420]: Cannot automatically perturb a torsion with multiple terms to different form. Please specify perturbed parameters manually for this torsion in your topology! So, I am trying to solve the problem converting the multiple dihedral definitions in the unique and equivalent Ryckaert-Bellemans. Is it in your opinion a correct idea? Is there any reference I can find where the conversion is easly explained? Thank you, Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] MARTINI parameters for dodecyl maltoside (DDM)
Hi Dariush, I've checked but it seems there no parameters for my detergent. Actully there are parameters for the polar head and the lipidic tail, so it is worth trying to merge them to have the correct representation! Francesco 2012/5/21 Dariush Mohammadyani d.mohammady...@gmail.com Have you checked MARTINI website? http://md.chem.rug.nl/cgmartini/index.php/downloads/force-field-parameters Dariush Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA On Sun, May 20, 2012 at 1:01 PM, francesco oteri francesco.ot...@gmail.com wrote: Dear gromacs users, does someone of you know whether parameters for the detergent dodecyl-beta-maltoside are avalaible in MARTINI forcefield? Thank you in advance, Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] constraints between protein ligand - metal chelation
You are right Peter 2012/5/21 Peter C. Lai p...@uab.edu This approach still requires the system to be parameterized as a single moleculetype, doesn't it? On 2012-05-20 04:42:26PM +0200, francesco oteri wrote: Hi, if you are able to define atom couples able to mantein the structure of your complex, you can insert in .top file a set of bond using function 6 (see table at pag 125 of the user manual). For example, let atom 1 and 100 are at distance 0.6nm, you can insert in .top a row like 1 100 6 0.6 1000 you impose a bond between the two atoms having as eauilibrium distance 0.6nm and force strenght 1000J. Function 6 doesn't implie the generation of angles and dihedrals so it is the right choice to impose distance restraints Francesco 2012/5/20 R.S.K.Vijayan biovija...@gmail.com Many thanks for your response. No special reasons for parametrizing the ligand and the protein as a separate system. I dont think that the ligand and protein can be parametrized as a single system, but will definitely try doing it as a single system and see if it works. Regards Vijayan.R On Sat, May 19, 2012 at 10:23 PM, Peter C. Lai p...@uab.edu wrote: Is there a particular reason why the ligand has been parameterized as a separate moleculetype from the protein in your case? I prefer to treat coordination bonds as real bonds instead of relying on electrostatic interactions anyway, since it is the only way to conservatively ensure the coordination geometry is preserved (like for Zn, where QM predicts a tetrahedral geometry but Zn free ions will result in an octahedral geometry). In any case, even if you stick with freeion Zn, you can paramaterize the complex as a single moleculetype and use distance restraints there, can't you? On 2012-05-19 09:42:25PM -0400, R.S.K.Vijayan wrote: Dear Gromacs users I was wondering if there exists any technique that sets distance restraint between specified ligand (atoms) and the protein(atoms) in Gromacs. I am simulating a system which contains metal ions coordinated to the Ligand. I looked in to the mailing list and Gromacs manual and figured out that *genrster* can be employed, to set distance, position and dihedral restraints. Unfortunately i also stumbled on the fact that restraints between systems is not possible. Since force fields are not good at handling chelation between metal atoms, i find that the metals drifting away from the coordinated ligand atoms during the course of simulation, hence i introduced position constraints for the metal and ended up realizing that the coordination distance between the ligand and the metal exceeds the permissible range and the angles between the chelating atoms gets distorted and some coordinating residues like Histidine and Aspartic acid also moves away from the metal. Hence, i was wondering if l anyone knows of any method (apart from QM/MM) that can help to set distance restraints between the protein (metal ion ) and the ligand, also any suggestion that could help in handling ligand metal chelation is welcomed. Thanking in advance Regards Vijayan.R -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808| == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support
Re: [gmx-users] constraints between protein ligand - metal chelation
Hi, if you are able to define atom couples able to mantein the structure of your complex, you can insert in .top file a set of bond using function 6 (see table at pag 125 of the user manual). For example, let atom 1 and 100 are at distance 0.6nm, you can insert in .top a row like 1 100 6 0.6 1000 you impose a bond between the two atoms having as eauilibrium distance 0.6nm and force strenght 1000J. Function 6 doesn't implie the generation of angles and dihedrals so it is the right choice to impose distance restraints Francesco 2012/5/20 R.S.K.Vijayan biovija...@gmail.com Many thanks for your response. No special reasons for parametrizing the ligand and the protein as a separate system. I dont think that the ligand and protein can be parametrized as a single system, but will definitely try doing it as a single system and see if it works. Regards Vijayan.R On Sat, May 19, 2012 at 10:23 PM, Peter C. Lai p...@uab.edu wrote: Is there a particular reason why the ligand has been parameterized as a separate moleculetype from the protein in your case? I prefer to treat coordination bonds as real bonds instead of relying on electrostatic interactions anyway, since it is the only way to conservatively ensure the coordination geometry is preserved (like for Zn, where QM predicts a tetrahedral geometry but Zn free ions will result in an octahedral geometry). In any case, even if you stick with freeion Zn, you can paramaterize the complex as a single moleculetype and use distance restraints there, can't you? On 2012-05-19 09:42:25PM -0400, R.S.K.Vijayan wrote: Dear Gromacs users I was wondering if there exists any technique that sets distance restraint between specified ligand (atoms) and the protein(atoms) in Gromacs. I am simulating a system which contains metal ions coordinated to the Ligand. I looked in to the mailing list and Gromacs manual and figured out that *genrster* can be employed, to set distance, position and dihedral restraints. Unfortunately i also stumbled on the fact that restraints between systems is not possible. Since force fields are not good at handling chelation between metal atoms, i find that the metals drifting away from the coordinated ligand atoms during the course of simulation, hence i introduced position constraints for the metal and ended up realizing that the coordination distance between the ligand and the metal exceeds the permissible range and the angles between the chelating atoms gets distorted and some coordinating residues like Histidine and Aspartic acid also moves away from the metal. Hence, i was wondering if l anyone knows of any method (apart from QM/MM) that can help to set distance restraints between the protein (metal ion ) and the ligand, also any suggestion that could help in handling ligand metal chelation is welcomed. Thanking in advance Regards Vijayan.R -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808| == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] MARTINI parameters for dodecyl maltoside (DDM)
Dear gromacs users, does someone of you know whether parameters for the detergent dodecyl-beta-maltoside are avalaible in MARTINI forcefield? Thank you in advance, Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] charm in gromacs
Hi, at the link http://dl.dropbox.com/u/40545409/charmm2itp.tgz you can find the files I am using Files ffcharmmnb.itp ffcharmmbon.itp have been generated through: convert_charmm_to_gromacs.pl par_all36_carb.prm while carbohydrates.rtp and carbohydrates.rtp through a script of mine. Now, if you look at [ dihedraltypes ] section in file ffcharmmbon.itp, there are strange things: 1) dihedrals defined once, are converted Ryckaert-Bellemans form, while the armonic form should be more clear. Anyway, it just a matter of style so I dont complan about. 2) dihedrals with multiple definitions ( OC30P CC3162 CC3161 OC311 at line 598 in file ffcharmmbon.itp, for example) are defined as: OC30P CC3162 CC3161 OC311 3 20.92 41.84 16.74 -41.84 0 0 ; 30P CC3162 CC3161 OC311 1 180 10.46 1 ; 30P CC3162 CC3161 OC311 1 0 8.368 2 ; 30P CC3162 CC3161 OC311 1 0 10.46 3 The commented lines clearly display the multiple definition, that can be described using function 9 3) An other problem rise with impropers dihedrals. Any of them are defined as Ryckaert-Bellemans, ex. HCA1 CC3161 CC3162 OC311 3 0.5858 1.757 0 -2.343 0 0 at line 926 of ffcharmmbon.itp while points 1 and 2 don't impact on the correctness of the simulation and can be bypassed defining [ bondedtypes ] section as following 1 5 321 3 1 0 Problem 3 cannot be solved without manipulating the ffcharmmbon.itp. In fact, since some impropers are defined as functiontype 2 other as functiontype 3, so there is not an unique bondedtypes definition covering both the definition. Did I any mistake or actually there is a problem in the script? Francesco 2012/5/18 Mark Abraham mark.abra...@anu.edu.au On 18/05/2012 2:52 AM, francesco oteri wrote: Dear gromacs users, I am trying to port a set of charm parameter in gromacs. I am using the script convert_charmm_to_gromacs.pl contained in the file charmm_to_gromacs.tgz ( http://www.gromacs.org/@api/deki/files/76/=charmm_to_gromacs.tgz). Regarding dihedrals, the entry regarding the file says that pdb2gmx cannot generate multiple periodic dihedral functions such as CHARMM uses for some dihedrals - these must be converted to Ryckaert-Bellemans functions, i.e. expressed as a cosine power expansion This assumption is no longer valid, is it? As far as I know, infact, now gromacs support multiple periodic function (funtion 9), is it? Correct, but with the inclusion of native CHARMM27 in GROMACS, I have had no reason to upgrade these conversion scripts to support function type 9. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: mixing Urey-Bradley and armonic in the same rtp file
Dear gromacs users, I think I solved the problem. I converted armonic angle potentials in the Urey-Bradley potentials using 0 as constant for the 1-3 bond potential. Is it right in your opinion? Francesco 2012/5/16 francesco oteri francesco.ot...@gmail.com Dear gromacs users, I am trying to port in gromacs the CHARMM36 all-atom carbohydrate force field. I downloaded the charmm files toppar_carb_apr12.tgz from http://mackerell.umaryland.edu/CHARMM_ff_params.html and I converted bonded and nonbonded parameters in gromacs format through the script convert_charmm_to_gromacs.pl. I have successfully generated the .top, using pdb2gmx, as well. But when I run grompp, it complains with errors like: *No default Angle types * * * and *No default Improper Dih. types* Look at the attacched file for the complete output from grompp. Now I inspected the missed interaction and, at least for the angle part, I figured out the problem. In the original charm parametrization there are angles parametrized as armonic and other angles parametrized as Urey-Bradley. Moreover, as far as I know, in the rtp file only one form can be used because of the [ bondedtypes ] clause. So my question is: Is there any way to mix, in the same residue (and hopefully in the same .rtp file), angles parametrized in the armonic form and Urey-Bradley parametrized angles? Is a correct solution parametrizing everything as armonic angles and mimic the bond potential between atom 1 and 3 present Urey-Bradley as a bond with same strenght and force value? Francesco -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Two [ dihedrals ] sections in topology
Hi 2012/5/17 Lara Bunte lara.bu...@yahoo.de Hi Just for correct understanding: In this empty [ dihedrals ] bock are 11 lines without equilibrium angle and force constant, that looks like: [ dihedrals ] ; aiajakal functc0c1 c2c3c4c5 2 119 8 2 6 8 910 2 Did this mean, that this are really physical dihedrals, that were given by pdb2gmx and the only reason that they are empty is, that they are not parametrized? Is this correct? No, it means that defaukt values (i.e. listed in [ dihedraltypes ] section ) will be applied Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkul jalem...@vt.edu An: Lara Bunte lara.bu...@yahoo.de; Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 17:02 Donnerstag, 17.Mai 2012 Betreff: Re: [gmx-users] Two [ dihedrals ] sections in topology On 5/17/12 10:48 AM, Lara Bunte wrote: Hi grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr gives me errors like ERROR 1 [file topol.top, line 233]: No default Improper Dih. types and so on. This line 233 is the starting of my empty [ dihedrals ] block. I erase it by hand out of my topology, so that only the correct [ dihedrals ] out of the .rtp and ffbonded.itp file are in the topology. After this grompp works without error and even without any warning. So the question how to force pdb2gmx to use only my [ dihedrals ] block is important for me, because I don't like to erase it always by hand out of the topol.top file. This goes back to something that has been stated several times now, and was discussed the other day. If pdb2gmx finds 4 atoms connected via bonds, it assigns a dihedral to it. That's just physically real. If your force field then doesn't have parameters for that particular interaction, you get the error shown above. That doesn't mean you should go deleting things until grompp works because what will result will likely be senseless. If your empty (which is not really empty, as we've been saying) dihedrals are causing the problems, then you need to add parameters for them in ffbonded.itp or in the topology itself, not hack the topology apart. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] charm in gromacs
Dear gromacs users, I am trying to port a set of charm parameter in gromacs. I am using the script convert_charmm_to_gromacs.pl contained in the file charmm_to_gromacs.tgz ( http://www.gromacs.org/@api/deki/files/76/=charmm_to_gromacs.tgz). Regarding dihedrals, the entry regarding the file says that pdb2gmx cannot generate multiple periodic dihedral functions such as CHARMM uses for some dihedrals - these must be converted to Ryckaert-Bellemans functions, i.e. expressed as a cosine power expansion This assumption is no longer valid, is it? As far as I know, infact, now gromacs support multiple periodic function (funtion 9), is it? Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] mixing Urey-Bradley and armonic in the same rtp file
Dear gromacs users, I am trying to port in gromacs the CHARMM36 all-atom carbohydrate force field. I downloaded the charmm files toppar_carb_apr12.tgz from http://mackerell.umaryland.edu/CHARMM_ff_params.html and I converted bonded and nonbonded parameters in gromacs format through the script convert_charmm_to_gromacs.pl. I have successfully generated the .top, using pdb2gmx, as well. But when I run grompp, it complains with errors like: *No default Angle types * * * and *No default Improper Dih. types* Look at the attacched file for the complete output from grompp. Now I inspected the missed interaction and, at least for the angle part, I figured out the problem. In the original charm parametrization there are angles parametrized as armonic and other angles parametrized as Urey-Bradley. Moreover, as far as I know, in the rtp file only one form can be used because of the [ bondedtypes ] clause. So my question is: Is there any way to mix, in the same residue (and hopefully in the same .rtp file), angles parametrized in the armonic form and Urey-Bradley parametrized angles? Is a correct solution parametrizing everything as armonic angles and mimic the bond potential between atom 1 and 3 present Urey-Bradley as a bond with same strenght and force value? Francesco grompp10.log Description: Binary data -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] poor performance in Hemiltonian Replica Exchange
Dear gromacs users, I performed a Hemiltonian Replica Exchange (i.e. replica exchange where each replica has a init_lambda=0, delta_lambda=0 and init_lambda ranging uniformely from 0 to 1). Since I have only ten fixed discrete lambda, I run a Temperature Replica Exchange where, for each replica I generated a .top file with the parameter rescaled through a python script ( in practice I did through python the same thing gromacs is supposed to do with the H-REM previously described). Now gromacs complained because every replica has the same setup, so I changed the temperatures using very close values (300.0001K, 300.0002K,300.0003K,300.0004K,300.0005K,300.0006K,300.0007K,300.0008K, 300.0009K) With this setup the simulation runs fine and I expect to have similar result. Then I compared the results observing two phenomena: 1) In the second case exchange rate is 100%, while in the first case I have an exchange rate close to 30%. Does it rise because the temperatures are too close? 2) The second setup is 3x faster! In particular I observe an imbalance between PME and force calculation ranging from 10% to 60%. I tried to run each replia indipendently (a different mdrun instance for each .tpr file) but still I observe the same performance slowdown. I guess the free energy impairs the efficient force calculation, but I dont understand why. Can someone explain me the two observations? Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] a question about ensemble
Hello, 2012/5/3 Dommert Florian domm...@icp.uni-stuttgart.de On Thu, 2012-05-03 at 07:32 +0200, Albert wrote: hello: I wondering are the three thermostat methods: Langevin, Berendsen and Nose-Hoover chain are all compatible with semi-isotropy coupling style? If I would like to use semi-isotropy coupling method, which one would be better? thank you very much Hi, what should be coupled in a semi-isotropic manner ? I assume the pressure and now the question is, which thermostat to apply, isn't it? The three mentioned barostats are all of different kinds. While Langevin provides a thermostating method for implicit solvent, the other mentioned Thermostats are based on an explicit atom description of the system. However, the Berendsen thermostat quite old and not symplectic, I remark that Langevin method is used also for explicit water system! which means that the phase space volume is not conserved. Fortunately, an updated method, the v-rescale thermostat of Bussi et al, has been published some years ago. It is quite similar to the Berendsen thermostat, but symplectic and suitable for production and equilibration. Finally the Nose-Hoover chain (NHC) is based on a extended Lagrangian for the system you want to simulate and corresponding equations of motions are applied in order to keep the temperature constant. NHC is symplectic, too, but not suitable for equilibration. However, as the only reasonable method for anisotropic pressure coupling is the Parrinello-Rahman (PR) barostat, or its extended version MTTK, which relies on the same idea as NHC, I would assume, that for production a combination of NHC and MTTK is a good choice. For the equilibration I would use a v-rescale thermostat and the Berendsen barostat, because PR and MTTK would take far too much time to achieve equilibrium. Hence, it much depends on the purpose, which combination of thermo- and barostat is the most suitable one. /Flo Anyway, I think that there is no strict coupling between temperature and pressure coupling: You need to keep the tempaerature fixed around a value and the same for pressure, so I guess any combination v-rescale, NHC, Langevin versus PR or MTTK is, in priciple, right. Maybe convergence speed changes, but in this case banchmark are quite useful very welcolme! best, Francesco best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] a question about ensemble
2012/5/3 Dommert Florian domm...@icp.uni-stuttgart.de On Thu, 2012-05-03 at 10:48 +0200, francesco oteri wrote: Hello, 2012/5/3 Dommert Florian domm...@icp.uni-stuttgart.de On Thu, 2012-05-03 at 07:32 +0200, Albert wrote: hello: I wondering are the three thermostat methods: Langevin, Berendsen and Nose-Hoover chain are all compatible with semi-isotropy coupling style? If I would like to use semi-isotropy coupling method, which one would be better? thank you very much Hi, what should be coupled in a semi-isotropic manner ? I assume the pressure and now the question is, which thermostat to apply, isn't it? The three mentioned barostats are all of different kinds. While Langevin provides a thermostating method for implicit solvent, the other mentioned Thermostats are based on an explicit atom description of the system. However, the Berendsen thermostat quite old and not symplectic, I remark that Langevin method is used also for explicit water system! But there a big question arises to me. The thermostatting by Langevin is achieved due to random kicks. If I simulate all atoms explicitly, there is only vacuum between the atoms. Where do the random kicks come from and how do I set gamma, which is actually related to the viscosity of the medium I am simulating in? If my medium is vacuum, then gamma should be zero, shouldn't it, and gamma=0 means no coupling, and hence, Newton's equation of motion are recovered. I am not an expert with the Langevin thermostat, so this are serious questions that arise to me now. Furthermore I also thought, that Langevin dynamics were exactly established for a description of a system within a medium. Implicit Implicit solvent means accounting for the solvent presence without including water atoms, look at http://en.wikipedia.org/wiki/Implicit_solvation for details. Regarding the collision source, it is water! The gamma value represent the average collision frequence experienced by a protein atoms against water in solution. You have no water, so it models the water presence. In implicit water simulation, usually a value close to 50 ps-1 (the experimental values) is used, while for explicit water is used a value around 2-5ps-1 bacause water is present so it actually collides with protein. /Flo which means that the phase space volume is not conserved. Fortunately, an updated method, the v-rescale thermostat of Bussi et al, has been published some years ago. It is quite similar to the Berendsen thermostat, but symplectic and suitable for production and equilibration. Finally the Nose-Hoover chain (NHC) is based on a extended Lagrangian for the system you want to simulate and corresponding equations of motions are applied in order to keep the temperature constant. NHC is symplectic, too, but not suitable for equilibration. However, as the only reasonable method for anisotropic pressure coupling is the Parrinello-Rahman (PR) barostat, or its extended version MTTK, which relies on the same idea as NHC, I would assume, that for production a combination of NHC and MTTK is a good choice. For the equilibration I would use a v-rescale thermostat and the Berendsen barostat, because PR and MTTK would take far too much time to achieve equilibrium. Hence, it much depends on the purpose, which combination of thermo- and barostat is the most suitable one. /Flo Anyway, I think that there is no strict coupling between temperature and pressure coupling: You need to keep the tempaerature fixed around a value and the same for pressure, so I guess any combination v-rescale, NHC, Langevin versus PR or MTTK is, in priciple, right. Maybe convergence speed changes, but in this case banchmark are quite useful very welcolme! best, Francesco best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Florian Dommert Dipl. - Phys. Institute
Re: [gmx-users] Lamb-Protein
Hi Justin, I have free-energy = no in my .mdp file, but I still see this value in g_energy. It should be absent or always 1 while the values by g_energy are close to 1 but still fluctuating along the trajectory. So, can you explain me how the value is used by gromacs? Francesco 2012/5/3 Justin A. Lemkul jalem...@vt.edu On 5/3/12 10:52 AM, francesco oteri wrote: Dear gromacs users, I am using g_energy to extract energies and I noticed that, amon the different groups, there groups like Lamb-Protein,Lamb-Water_and_**ions and other names I dont know. I am wondering whether exist a guide explaining the differet contribution displayed by g_energy; Most are fairly obvious, others are discussed on gromacs.org. In the case of Lamb- terms, these are the lambda values when the free energy code is being utilized. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to extract trajectories into individual pdb file?
In particular, look at the option -sep 2012/5/3 Mark Abraham mark.abra...@anu.edu.au On 4/05/2012 1:10 AM, Albert wrote: hello: I've finished a MD job and I am wondering how can we extract individual pdb from trajectories in Gromacs? each time I always get a single pdb contains lots of snapshots. See trjconv -h Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to extract trajectories into individual pdb file?
-fit 2012/5/3 Albert mailmd2...@gmail.com On 05/03/2012 05:12 PM, francesco oteri wrote: In particular, look at the option -sep thank you for kind reply. but how to superimposed the left snapshot with the first one? thanks again for helps -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Making Disulfide Bonds
Hi James, usually people run a minimization using distance restrain on the two atoms in order to make them closer. Then the obtained cnfiguration is used to recalculate the topology. Francesco 2012/4/28 James Starlight jmsstarli...@gmail.com Dear Gromacs Users! I have a model of my protein wich has 4 S-S bounds in the loop regions. So I want to define in topology all those four S-S linkage. Unfortunatelly one of that S-S have not been recognised by Gromacs ( Also I've tried to check this bond in pymol and found that distance between that two Cys Cys are larger for S-S occurence) due to some inaccyracy of model. Is there any way to define such missing S-S manually? On the gromacs site I've found possible sollution by means of spechbond.dat editing. I've tried to increase distance between S-S atoms but this have not had desirebly affect. In the topology.top file I've found that the S-S bonds beetween S atoms are defined in the bond section without any type for such bond type. Also I've found that the same enties are present in the angle and dihedralls sections. Could I define the same contact only in the bond section and further minimise my system to obtain new S-S linckage or should I also define all other enties ( like dihedralls etc) for that bond ? Thanks for help James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Making Disulfide Bonds
Hi James, usually I insert by hand a bond in the topology file between the two atoms and then I minimize. This bond doesn't cause the generataion of angles and dihedrals, butit is enough to make the atom closer. Francesco Il 28/04/2012 16:08, James Starlight ha scritto: .. and the main question- what should be in mdp file of such restrained minimisation ? Today I've done vry properly minimisation of such system in vacuum with the CG minimisator and applied disres ( above example ) with big force constant ( disres options have been defined in the minim.mdp file ). As the result I have not noticed any perturbation in the distance between two S-S atoms the distance between wich I've constrained. 2012/4/28 James Starlight jmsstarli...@gmail.com mailto:jmsstarli...@gmail.com Hi Francesco! So I must define in the current topology the disres bettwen two S atoms ( in the below example 1 and 10 ) to apply hormonic restains [ distance_restraints ] ; ai aj type index type' low up1 up2 fac 1 10 10 10.18 0.20 0.22 1.0 to restrain this atoms within 0.2 nm. Does it correct ? Or should I use some other disres for such task ? James 2012/4/28 francesco oteri francesco.ot...@gmail.com mailto:francesco.ot...@gmail.com Hi James, usually people run a minimization using distance restrain on the two atoms in order to make them closer. Then the obtained cnfiguration is used to recalculate the topology. Francesco 2012/4/28 James Starlight jmsstarli...@gmail.com mailto:jmsstarli...@gmail.com Dear Gromacs Users! I have a model of my protein wich has 4 S-S bounds in the loop regions. So I want to define in topology all those four S-S linkage. Unfortunatelly one of that S-S have not been recognised by Gromacs ( Also I've tried to check this bond in pymol and found that distance between that two Cys Cys are larger for S-S occurence) due to some inaccyracy of model. Is there any way to define such missing S-S manually? On the gromacs site I've found possible sollution by means of spechbond.dat editing. I've tried to increase distance between S-S atoms but this have not had desirebly affect. In the topology.top file I've found that the S-S bonds beetween S atoms are defined in the bond section without any type for such bond type. Also I've found that the same enties are present in the angle and dihedralls sections. Could I define the same contact only in the bond section and further minimise my system to obtain new S-S linckage or should I also define all other enties ( like dihedralls etc) for that bond ? Thanks for help James -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Velocities in trjconv 4.5.5
Hi Ignacio, actually .cpt contains velocities and, to extract a .gro containing them, you can try to use editconf. Francesco Il giorno 23 aprile 2012 16:45, Ignacio Fernández Galván jel...@yahoo.comha scritto: --- On Mon, 23/4/12, Alex Marshall amars...@uwo.ca wrote: I'm pretty sure .cpt files don't store velocity information. Try using a trr file instead. Well, I'm pretty sure .cpt files do store velocities: 1. What good would be checkpoint files without velocities? 2. It works with version 4.5.3 3. gmxcheck -f file.cpt says, for both 4.5.3 and 4.5.5: Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] problem with hemiltonian replica exchange restarting
Dear gromacs users, I run a REMD simulation 20ns long, enabling free energy and using a different init_lambda value for each replica and using gromacs 4.5.3. I run the simulation on a cluster equipped with torque queue management. 1) I used the following command in the submission script: mpirun -np $NP mdrun_mpi_gcc -s rest2_.tpr -multi 10 -replex 1000 -dd 2 2 2 -maxh 36 -v log.rest2_TrpCage The run went fine and it correctly terminated in 36 hours, before reaching the 20ns and writing each file. 2) Then I extended the simulation using the command: mpirun -np $NP mdrun_mpi_gcc -s rest2_.tpr -multi 10 -replex 1000 -dd 2 2 2 -maxh 36 -cpi -v log.resume.rest2_TrpCage This time, the program crashed with the error: *[[28079,1],72][/caspur/shared/src/openmpi/openmpi-1.4.3/ompi/mca/btl/openib/btl_openib_component.c:3227:handle_wc] from neo085 to: neo098 error polling LP CQ with status RETRY EXCEEDED ERROR status number 12 for wr_id 427787264 opcode 36099 vendor error 129 qp_idx 0 * *--* *The InfiniBand retry count between two MPI processes has been* *exceeded. Retry count is defined in the InfiniBand spec 1.2* *(section 12.7.38):* * * *The total number of times that the sender wishes the receiver to* *retry timeout, packet sequence, etc. errors before posting a* *completion error.* * * *This error typically means that there is something awry within the* *InfiniBand fabric itself. You should note the hosts on which this* *error has occurred; it has been observed that rebooting or removing a* *particular host from the job can sometimes resolve this issue.* * * *Two MCA parameters can be used to control Open MPI's behavior with* *respect to the retry count:* * * ** btl_openib_ib_retry_count - The number of times the sender will* * attempt to retry (defaulted to 7, the maximum value).* ** btl_openib_ib_timeout - The local ACK timeout parameter (defaulted* * to 10). The actual timeout value used is calculated as:* * * * 4.096 microseconds * (2^btl_openib_ib_timeout)* * * * See the InfiniBand spec 1.2 (section 12.7.34) for more details.* * * *Below is some information about the host that raised the error and the* *peer to which it was connected:* * * * Local host: neo085* * Local device: mthca0* * Peer host:neo098* * * *You may need to consult with your system administrator to get this* *problem fixed.* *--* *--* *mpirun has exited due to process rank 72 with PID 2083 on* *node neo085 exiting without calling finalize. This may* *have caused other processes in the application to be* *terminated by signals sent by mpirun (as reported here).* *--* *mpirun: abort is already in progress...hit ctrl-c again to forcibly terminate* The reached simulation time written in the md0.log file was *12.0766 ns* 3) I assumed it was a network error, imparing the correct comunication among the nodes. I frequently obtain this error and usually I restart the simulation without any troube. Hence I restarted again the simulation: mpirun -np $NP mdrun_mpi_gcc -s rest2_.tpr -multi 10 -replex 1000 -dd 2 2 2 -maxh 36 -cpi -v log.resume1.rest2_TrpCage The simulation went fine, reaching the 20ns and without any complains by gromacs. When I started the data analysis, I noticed that all the 10 trajectory files are nearly *12.07ns, *while energy files are 20ns long. if I check the last modification time by ls -l it says me that the files has been modified nearly simultaneously: [oteri@matrix2 REST2]$ ls -lrt *.trr *.edr -rw-r--r-- 1 oteri be7 1175659492 avr 19 15:52 traj8.trr -rw-r--r-- 1 oteri be7 1175659492 avr 19 15:52 traj3.trr -rw-r--r-- 1 oteri be7 1175659492 avr 19 15:52 traj2.trr -rw-r--r-- 1 oteri be7 1175659492 avr 19 15:52 traj1.trr -rw-r--r-- 1 oteri be7 1175659492 avr 19 15:52 traj7.trr -rw-r--r-- 1 oteri be7 1175659492 avr 19 15:52 traj9.trr -rw-r--r-- 1 oteri be7 1175659492 avr 19 15:52 traj4.trr -rw-r--r-- 1 oteri be7 1175659492 avr 19 15:52 traj6.trr -rw-r--r-- 1 oteri be7 1175659492 avr 19 15:52 traj0.trr -rw-r--r-- 1 oteri be7 1175659492 avr 19 15:52 traj5.trr -rw-r--r-- 1 oteri be71201324 avr 19 15:52 ener9.edr -rw-r--r-- 1 oteri be71201324 avr 19 15:52 ener8.edr -rw-r--r-- 1 oteri be71201324 avr 19 15:52 ener7.edr -rw-r--r-- 1 oteri be71201324 avr 19 15:52 ener6.edr -rw-r--r-- 1 oteri be71201324 avr 19 15:52 ener5.edr -rw-r--r-- 1 oteri be71201324 avr 19 15:52 ener4.edr -rw-r--r-- 1 oteri be71201324 avr 19 15:52 ener3.edr -rw-r--r-- 1 oteri be71201324 avr 19 15:52 ener2.edr -rw-r--r-- 1 oteri be71201324 avr 19 15:52 ener1.edr -rw-r--r-- 1 oteri be71201324 avr 19 15:52 ener0.edr So actually, gromacs accessed to both trajectory and energy files. I have
Re: [gmx-users] Best Force Field for a Membrane Protein
Hi Anirban, as far as I know the best force-field for membrane protein system is Charm36: it uses Charm27 for proteins but an improved parametrization for membrane lipids. I don't know if the lipids part has been already ported in gromacs format, but is a trivial task you can do in 1-2 days. Francesco Il giorno 19 aprile 2012 08:32, Anirban Ghosh reach.anirban.gh...@gmail.com ha scritto: Hi ALL, When running a membrane protein (say GPCR) in a lipid bilayer (say POPC or DPPC etc.) which according to your experience is the most suited force-field in GROMACS that best retains the 7TM / secondary structures of the protein over long simulations? I have tried running with ff53a6 (as suggested in Justin's tutorial), but find that the helices in the bilayer tend to lose their helicity over time and turns into coils. ff43a2 seems to do the job somewhat better by retaining the helicity. Will ff43a1 work even better as the principle aim is to observe changes in the protein without losing its secondary structures? Your experience please. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Fe atom problems....in simulation
Hi, You have to had LJ parameters in ffnonbonded.itp file in the subfolder relative to your force-field Francesco Il giorno 16 aprile 2012 11:08, Kamalesh Roy roy.kamales...@gmail.com ha scritto: CAn any one siggest me how can I run simulation a protein containing Fe atom, I have changed the iions.itpfile and included there Fe in residue type.dat bu still it is returning an error. FE parameter not found. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] progressive imbalance in REMD
Hi Marc, actually I am running NVT REMD so particle density is more or less constant along differet replicas. Is there any way to test which term takes more to be carried out? Francesco Il 13/04/2012 18:02, Mark Abraham ha scritto: On 14/04/2012 1:46 AM, francesco oteri wrote: Dear gromacs users, I am running REMD through gromacs 4.5.5 using 10replicas. I am experiencing a problem with simulation efficiency, in particular from gromacs output, like the following: vol 0.49 imb F 4% vol 0.64 imb F 8% vol 0.17 imb F 2% vol 0.56 imb F 10% vol 0.17! imb F 7% vol 0.75 imb F 11% vol 0.45 imb F 11% vol 0.13! imb F 8% vol 0.45 imb F 16% vol 0.55 imb F 23% step 735900, will finish Mon Apr 16 07:29:53 2012 it seems that higher temperature replicas suffer of an higher imbalance between force and PME. These are the average values: 4.58991117815 5.5175129881 6.32679738562 7.21887045416 8.1979219038 9.45466733702 10.9115133233 12.5899111781 15.0987095693 19.5630970337 Of course this problem impacts on overall performances. My questions are: 1) Is the progressive imbalance expected? 2) Is there any way to alleviate the problem? Guessing wildly in the absence of a description, you're running NPT REMD, and so the particle density changes with T, so the nonbonded cost varies with T while the PME cost does not. The timing breakdown at the end of the individual .log files may prove informative in this respect. This problem snowballs - your generalized ensemble can only progress at the rate of your slowest contributing ensemble. In theory, one could develop a scheme where the PME performance and accuracy was near-constant with respect to T by varying the cutoff, splitting parameter and Fourier grid, but since most people choose their PME parameters by copying people who pulled near-arbitrary numbers out of the air, this would seem to be overkill. People often do NVT REMD to avoid this effect if they are interested only in the ensemble at one temperature. That means the higher-temperature replicas have unphysically high pressures, which might or might not prove to be useful for enhanced sampling. Some people think that makes the sampling at the low temperature bogus, but I have never seen a convincing argument that all the replicas should correspond to a physical ensemble that closely resembles the target ensemble. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] File editing - only one layer of water around a molecule
Hi Lara, the simplest way is using vmd. Briefly, 1) load the pdb file in vmd. 2) create a representation using a string like: same residue as within 3. of protein. where protein is the group around the molecule you have to use, I used protein just as example Il giorno 13 aprile 2012 11:29, Lara Bunte lara.bu...@yahoo.de ha scritto: I read g_select -select 'help all' and I understand nothing of that. In general one have a molecule (valences closed by hydrogen) and a water box around it. How to select only the protein with the first water layers, say one layer? Please give me an example how to do this with gromacs. I read the examples in g_select -select 'help all' and I have no Idea what they are talking about. Thanks for help Greetings Lara -- *Von:* Mark Abraham mark.abra...@anu.edu.au *An:* Discussion list for GROMACS users gmx-users@gromacs.org *Gesendet:* 19:26 Mittwoch, 11.April 2012 *Betreff:* Re: [gmx-users] File editing - only one layer of water around a molecule On 12/04/2012 3:24 AM, Justin A. Lemkul wrote: Lara Bunte wrote: Could you please give how g_select is used? Reading g_select -h might have led you to try g_select -select 'help' Is there a tutorial for that? g_select -select 'help all' The information contained therein is very extensive, so be sure to read it thoroughly. It will fill several terminal windows explaining the syntax and providing examples. ... and search Google for some examples. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] File editing - only one layer of water around a molecule
Hi Lara, I sent an incomplete mail by error :( I was saying that the simplest way is using vmd. Briefly, 1) load the pdb file in vmd. 2) create a representation using a string like: same residue as within 3. of protein. where protein is the group around the molecule you have to use, I used protein just as example 3. is the cutoff distance between protein and any other ATOM in the system 3) same residue for each atom at point 2) it takes the corresponding residue avoiding residue bracking. If your pdb is more complex, but you need only water try: water and (same residue as within 3. of protein). Now you can visually inspect your selection and adjusting the distance. When everything is fine, you can save it through vmd save comman: 1) in the command line write: [atomselect top same residue as within 3. of protein] writepdb out.pdb It should work and it should make the work easier! Francesco Il giorno 13 aprile 2012 11:38, francesco oteri francesco.ot...@gmail.comha scritto: Hi Lara, the simplest way is using vmd. Briefly, 1) load the pdb file in vmd. 2) create a representation using a string like: same residue as within 3. of protein. where protein is the group around the molecule you have to use, I used protein just as example Il giorno 13 aprile 2012 11:29, Lara Bunte lara.bu...@yahoo.de ha scritto: I read g_select -select 'help all' and I understand nothing of that. In general one have a molecule (valences closed by hydrogen) and a water box around it. How to select only the protein with the first water layers, say one layer? Please give me an example how to do this with gromacs. I read the examples in g_select -select 'help all' and I have no Idea what they are talking about. Thanks for help Greetings Lara -- *Von:* Mark Abraham mark.abra...@anu.edu.au *An:* Discussion list for GROMACS users gmx-users@gromacs.org *Gesendet:* 19:26 Mittwoch, 11.April 2012 *Betreff:* Re: [gmx-users] File editing - only one layer of water around a molecule On 12/04/2012 3:24 AM, Justin A. Lemkul wrote: Lara Bunte wrote: Could you please give how g_select is used? Reading g_select -h might have led you to try g_select -select 'help' Is there a tutorial for that? g_select -select 'help all' The information contained therein is very extensive, so be sure to read it thoroughly. It will fill several terminal windows explaining the syntax and providing examples. ... and search Google for some examples. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] progressive imbalance in REMD
Dear gromacs users, I am running REMD through gromacs 4.5.5 using 10replicas. I am experiencing a problem with simulation efficiency, in particular from gromacs output, like the following: vol 0.49 imb F 4% vol 0.64 imb F 8% vol 0.17 imb F 2% vol 0.56 imb F 10% vol 0.17! imb F 7% vol 0.75 imb F 11% vol 0.45 imb F 11% vol 0.13! imb F 8% vol 0.45 imb F 16% vol 0.55 imb F 23% step 735900, will finish Mon Apr 16 07:29:53 2012 it seems that higher temperature replicas suffer of an higher imbalance between force and PME. These are the average values: 4.58991117815 5.5175129881 6.32679738562 7.21887045416 8.1979219038 9.45466733702 10.9115133233 12.5899111781 15.0987095693 19.5630970337 Of course this problem impacts on overall performances. My questions are: 1) Is the progressive imbalance expected? 2) Is there any way to alleviate the problem? Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how pdb2gmx calculate the total charge of a protein
Dear Acoot, the error, I guess, is you assumed the histidines are positive while I think they are neutral. Since the His protonation state is hard to identify at ph7, Hystidines are usually neutral. Francesco Il 07/04/2012 09:42, Acoot Brett ha scritto: Dear All, I have a protein, the charged residue numbers in the protein is as following ARG 11 ASP 19 glu 25 his 8 lys 24 asp+glu= 44 arg+his+lys=43 However the total charge of the protein given by pdb2gmx is -9. Will you please introduce to me how pdb2gmx calculate the total charge of the protein? Cheers, Acoot -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] REMD equilibration
Dear gromacs users, I have to perform REMD simulation, but since it is the first time I apply this tecnique I have a question regarding system equilibration. As far as I know, befaore starting the REMD each replica has to be equlibrated. The equilibration has to be carried out in the NPT ensemble or only in the NVT? Thanks in advance, Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] REMD equilibration
I understand, I am planning to run REMD between 300 and 600 K, so I think it is better equlibrating in NVT ensemble because at high temperature water evaporates, is it? Francesco Il giorno 23 marzo 2012 10:53, Kukol, Andreas a.ku...@herts.ac.uk ha scritto: Hi Francesco, It should be the same ensemble, in which you want to carry out the production REMD. Andreas From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of francesco oteri Sent: 23 March 2012 09:41 To: Discussion list for GROMACS users Subject: [gmx-users] REMD equilibration Dear gromacs users, I have to perform REMD simulation, but since it is the first time I apply this tecnique I have a question regarding system equilibration. As far as I know, befaore starting the REMD each replica has to be equlibrated. The equilibration has to be carried out in the NPT ensemble or only in the NVT? Thanks in advance, Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problem in oplsaa ffbonded.itp
OK, but for some AMBER dihedral the same goal has been obtained using an X for i and l atoms, like: X FE SS X 9 0.000.0 4 Why the same approach wasn't used for OPLSAA? Il giorno 21 marzo 2012 11:35, Justin A. Lemkul jalem...@vt.edu ha scritto: francesco oteri wrote: Dear Gromacs users, I am working on a program that need topology parsing. I am using the OPLSAA forcefield and I noticed that in ffbonded.itp file belonging to this force field there are these strange lines: [ dihedraltypes ] ; ijkl func coefficients ; Added DvdS for Quartz simulations SI OS1 0.000 3.766 3 SI OH1 0.000 3.766 3 If it describes dihedral definition, how is possible having only two atom types? Those are the central two atoms in the dihedral, i.e. atoms j and k in the i-j-k-l notation for a dihedral. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] bond managment in grompp
Dear gromacs user, I noted a strange behavior in topology generation workflow. I have a protein whose active site contains a Ni atom linked to 4 Cys. I inserted the 4 bonds by specbonds.dat. When I run pdb2gmx, I have inspected the Linking messages and they fit with the expected topology, I mean pdb2gmx correctly detects the four bonds nickel-sulphur. So I run grompp and the topol.tpr has been correctly generated. Then I compared topol.top and topol.tpr bonds and I noticed that in topol.top there a lot of fake-bonds, i.e Ni-hydrogen, Ni-Carbonium. I dumped topol.tpr through gmxdump, and I noticed that these bonds are no more present and only right bonds are present. So, I am wondering why the fake bonds are inserted in topol.top and how grompp detectes these bonds. Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] bond managment in grompp
CSB HA 9696 0.09 1.008 ; qtot -2.778 9697CT2607CSB CB 9697 -0.05 12.011 ; qtot -2.828 9698 HA607CSBHB1 9698 0.051 1.008 ; qtot -2.777 9699 HA607CSBHB2 9699 0.051 1.008 ; qtot -2.726 9700 S607CSB SG 9700 -0.57 32.06 ; qtot -3.296 9701 C607CSB C 9701 0.51 12.011 ; qtot -2.786 9702 O607CSB O 9702 -0.51 15.999 ; qtot -3.296 ; residue 610 CSA rtp CSA q -0.3 9732NH1610CSA N 9732 -0.47 14.007 ; qtot -3.766 9733 H610CSA HN 9733 0.31 1.008 ; qtot -3.456 9734CT1610CSA CA 9734 0.07 12.011 ; qtot -3.386 9735 HB610CSA HA 9735 0.09 1.008 ; qtot -3.296 9736CT2610CSA CB 9736 -0.03 12.011 ; qtot -3.326 9737 HA610CSAHB1 9737 0.08 1.008 ; qtot -3.246 9738 HA610CSAHB2 9738 0.08 1.008 ; qtot -3.166 9739 S610CSA SG 9739 -0.39 32.06 ; qtot -3.556 9740 C610CSA C 9740 0.51 12.011 ; qtot -3.046 9741 O610CSA O 9741 -0.51 15.999 ; qtot -3.556 ; residue 615 NI rtp NI q +0.4 9786 NI615 NI NI 97860.458.6934 ; qtot -3.926 ; residue 616 CN rtp CN q -0.5 9787 C616 CN C1 9787 0.11 12.011 ; qtot -3.816 9788 N616 CN N1 9788 -0.61 14.007 ; qtot -4.426 ; residue 617 CN rtp CN q -0.5 9789 C617 CN C1 9789 0.11 12.011 ; qtot -4.316 9790 N617 CN N1 9790 -0.61 14.007 ; qtot -4.926 ; residue 618 CO rtp CO q -0.1 9791 C618 CO C1 9791 0.22 12.011 ; qtot -4.706 9792 O618 CO O1 9792 -0.294 15.999 ; qtot -5 While this are the bonds I am referring: 1017 9786 1 1050 9786 1 9700 9786 1 9739 9786 1 1012 9786 1 * 1015 9786 1 * 1016 9786 1 * 1045 9786 1 * 1048 9786 1 * 1049 9786 1 * 9695 9786 1 * 9698 9786 1 * 9699 9786 1 * 9734 9786 1 * 9737 9786 1 * 9738 9786 1 * 9786 9787 1 9786 9789 1 9786 9791 1 The bonds with the * are what I call fake. i.e the couple 1012 9786 involves a bond between the nickel atom and an hydrogen. This couple, as well as the other fake couples, disappears in the .tpr file an interestingly pdb2gmx doesn't signal them. If the phenomena is not yet known, I can give you the data I used to generate the .top and .tpr. Francesco Il giorno 21 marzo 2012 16:18, Mark Abraham mark.abra...@anu.edu.au ha scritto: On 22/03/2012 1:46 AM, francesco oteri wrote: Dear gromacs user, I noted a strange behavior in topology generation workflow. I have a protein whose active site contains a Ni atom linked to 4 Cys. I inserted the 4 bonds by specbonds.dat. When I run pdb2gmx, I have inspected the Linking messages and they fit with the expected topology, I mean pdb2gmx correctly detects the four bonds nickel-sulphur. So I run grompp and the topol.tpr has been correctly generated. Then I compared topol.top and topol.tpr bonds and I noticed that in topol.top there a lot of fake-bonds, i.e Ni-hydrogen, Ni-Carbonium. Can you show an example of what you interpret as a fake bond? Mark I dumped topol.tpr through gmxdump, and I noticed that these bonds are no more present and only right bonds are present. So, I am wondering why the fake bonds are inserted in topol.top and how grompp detectes these bonds. Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Structural features for LINCS application
Il 16/03/2012 01:38, Mark Abraham ha scritto: On 16/03/2012 6:02 AM, Francesco Oteri wrote: Dear gromacs users, I am trying to simulate a protein (containing FeS cluster and a complex metal active site) using virtual site. I've to face a problem with LINCS. In particular, if I constrain only h-bonds without using virtual site, simulation runs fine but constraining all-bonds, simulation crashes after a lot of LINCS warning like: Step 356, time 0.712 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.408533, max 8.159325 (between atoms 2750 and 2754) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2750 2754 90.00.1365 1.2502 0.1365 In both cases simulation conditions are the same. The bonds causing problem belongs to the active site. I am wondering if there are structural features imparing the use of all-bonds constraints in LINCS. A second question is, how can I run MD with virtual site without all-bonds options. Coupled constraints, such as you might have in a cluster, can be delicate. Equilibrating with a quite small time step can be necessary. Mark Hi Mark, I've run 100ps at 0.5fs, and 1fs...but when I switch to 2fs it crashes. I've read in the manual and it seem that triangular structures might introduce problem, but I dont have such a structure in my protein. So, there are other coupled constraint that may cause problem in LINCS? Is it possible that the force constants can cause problem? Or anyway, is it possible using virtual site constraining only h-bonds? Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Structural features for LINCS application
Dear gromacs users, I am trying to simulate a protein (containing FeS cluster and a complex metal active site) using virtual site. I've to face a problem with LINCS. In particular, if I constrain only h-bonds without using virtual site, simulation runs fine but constraining all-bonds, simulation crashes after a lot of LINCS warning like: Step 356, time 0.712 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.408533, max 8.159325 (between atoms 2750 and 2754) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2750 2754 90.00.1365 1.2502 0.1365 In both cases simulation conditions are the same. The bonds causing problem belongs to the active site. I am wondering if there are structural features imparing the use of all-bonds constraints in LINCS. A second question is, how can I run MD with virtual site without all-bonds options. Thank you, Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Resources on simulation walls
Hi Andrew, at http://manual.gromacs.org/online/mdp_opt.html#nl the manual says: Without walls or with only one wall the system size is infinite in the z direction. Therefore pressure coupling or Ewald summation methods can not be used. These disadvantages do not apply when two walls are used So I guess wall are physical walls, i.e. something limitating the expansion of your system in the z-direction. In the xy plane the system is replicated because of pbc but, without walls, it would be unlimited in the z-direction. Il 10/03/2012 17:46, Andrew DeYoung ha scritto: Hi, Only if you have time, do you know of any resources that explain the concept of a Gromacs wall, which seems related to 2-D Ewald summation? In the Gromacs 4.5.4 manual, the parameters related to walls are described on page 182, and also on http://manual.gromacs.org/current/online/mdp_opt.html#walls . But do you know of any general explanations, books, or literature papers that would help me to understand what a wall does and why and when I need to use them? I cannot seem to find them discussed in the main Gromacs papers ( http://www.gromacs.org/Documentation/Gromacs_papers ). Also, is there another name for a simulation wall? When I use Google to search for MD simulation wall, it is not clear that I am looking for the correct thing. Thanks so much for your time. Andrew DeYoung Carnegie Mellon University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Fwd: charm to gromacs
Actually I solved the problem, I did a mistake in the bond conversion. Actually I found the right formula: k_gromacs = k_charmm**418.4**2 rising form the conversion from angstrom to nanometer -- Messaggio inoltrato -- Da: francesco oteri francesco.ot...@gmail.com Date: 08 marzo 2012 10:49 Oggetto: charm to gromacs A: Discussion list for GROMACS users gmx-users@gromacs.org Dear gromacs users, I am trying to convert a charmm style parameter file into gromacs. So I al trying to understand how converting the force constants from CHARMM to gromacs. Using the CHARMM27 force field as a reference, I've noticed that to convert the bond constant the following formula is supposed to be used: k_gromacs = k_charmm**4184**2 In fact if I try to convert the following line from par_all27_prot_lipid.prm charmm file: CEL1 CEL1 440.000 1.340 ! butene, yin,adm jr., 12/95 I obtain the right result ( 440.000*4184*2. = 368192.0) charmm27/ffbonded.itpCEL1CEL11 0.134 368192.0 But to convert the angle constants I've to use the following formula: k_gromacs = k_charmm**4.184**2. how demostrated by the conversion of the following line: par_all27_prot_lipid.prm CEL1CEL1CTL2 48.00 123.50 ! from 2-butene, yin,adm jr., 12/95 into charmm27/ffbonded.itp CEL1CEL1CTL25 123.50 401.664 0.0 0.0 My question is: Why in the former case I need the constant 4184 while in the latter the constant 4.184 is supposed to be used? Am I miss something? -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to input multiple trr files?
Gromacs is able to load you AMBER trajectory so you don't need to perform any conversion -- Messaggio inoltrato -- Da: a a pat...@hotmail.com Date: 08 marzo 2012 11:46 Oggetto: RE: [gmx-users] How to input multiple trr files? A: gmx-users@gromacs.org Dear Mark, In fact, I was converting the AMBER trajectories to trr format by VMD. However, my VMD is failed to load so large trajectories files. I guess I can convert several trr files into one trr file. Is it possible to be done with GROMACS? If yes, how can I do it? Many thanks, Catherine -- From: mark.abra...@anu.edu.au To: gmx-users@gromacs.org Date: Thu, 8 Mar 2012 21:36:03 +1100 Subject: Re: [gmx-users] How to input multiple trr files? On 08/03/12, *a a *pat...@hotmail.com wrote: Dear Gromacs experts, I am trying to use the following command: g_covar -s file.pdb -f dynamic.trr -o -v However, since my trr file is too large, I have to separately prepared it into dynamic1.trr dynamic2.trr, dynamic3.trr. Would you mind to instruct how to input several trr files, how to modify the above command line? This is not possible. Input to all GROMACS tools must be in one file, with rare exceptions for algorithms that do the same thing on several files. Either you need a filesystem capable of dealing with the large file, or follow the advice here http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] a request regarding pdb2gmx and specbond.dat
Hi, I agree it could be very useful. You can insert the bond hand-coding it in the topology, but you need also to generate angle and dihedral. This is very boring and error prone. Francesco Il giorno 08 marzo 2012 12:32, Ehud Schreiber schr...@compugen.co.il ha scritto: Hi, ** ** The mechanism for specifying special bonds for the pdb2gmx program, using the specbond.dat file (manual section 5.6.7), seems to me not general enough. The characteristic length of the bond is specifiable, but the range of lengths for which a bond is assumed is hardcoded as +-10% of the characteristic length. I, for example, am perturbing structures using the Concoord method, and lengths of disulfide bonds sometimes vary by more than 10%. I therefore suggest that two values would be added at the end of the line declaring a special bond, specifying the minimum and maximum lengths. These two values would be optional, so as not to break the existing arrangement, which would remain as the default. This should not require more than a few extra lines of code and would be, in my opinion, very useful. ** ** What do you say? ** ** Thanks, Ehud Schreiber. ** ** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Read mdcrd from AMBER --- Error Message
Hi Catherine, you should install any gromacs *4.5.x*, and then you can use gromacs with each trajectory supported by VMD because gromacs is able to use VMD plugin to perform trajectory reading. Basically: 1) Install the latest gromacs version 2) Install VMD 3) Set the variable VMD_PLUGIN_PATH to contain the complete path of the molfile vmd directory. In my case, for example: VMD_PLUGIN_PATH=/apps/vmd/1.9/**lib/vmd /plugins/LINUXAMD64/**molfile Francesco Il giorno 08 marzo 2012 17:40, a a pat...@hotmail.com ha scritto: Dear Sir/Madam, I learnt that we can use mdcrd from AMBER directly. I have used the following commands. /share1/gromacs/bin/g_covar -s xxx.pdb -f xxx.mdcrd -o -v An error message was obtained. Program g_covar, VERSION 4.0.7 Source code file: gmxfio.c, line: 737 Can not open file: md0.mdcrd.xtc Did I do anything wrong? Best regards, Catherine -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] LINCS problem with EM and Virtual sites
Hi gromacs users, I am tying to minimize a protein through grolacs 4.5.5 double precision. If I try to minimize it without virtual site, everythin goes fine but if I add virtual site through: pdb2gmx -vsite hydrogens -chainsep id -f Aqui_model.pdb -ff charmm27 -water tip3p -posrefc 1000 -v -rtpres I obtain the following output: *Steepest Descents:* * Tolerance (Fmax) = 1.0e+03* * Number of steps= 1000* *Step=0, Dmax= 1.0e-02 nm, Epot= 1.21621e+06 Fmax= 2.24275e+08, atom= 12592* *Step=1, Dmax= 1.0e-02 nm, Epot= -4.92685e+05 Fmax= 1.05309e+07, atom= 12585* *Step=2, Dmax= 1.2e-02 nm, Epot= -6.65927e+05 Fmax= 2.33570e+06, atom= 12586* *Step=3, Dmax= 1.4e-02 nm, Epot= -7.19859e+05 Fmax= 2.16295e+06, atom= 12585* *Step=4, Dmax= 1.7e-02 nm, Epot= -7.53908e+05 Fmax= 8.32452e+05, atom= 12586* *Step=5, Dmax= 2.1e-02 nm, Epot= -7.75691e+05 Fmax= 9.90803e+05, atom= 12585* *Step=6, Dmax= 2.5e-02 nm, Epot= -7.98119e+05 Fmax= 9.99586e+04, atom= 12730* *Step=7, Dmax= 3.0e-02 nm, Epot= -8.47120e+05 Fmax= 7.37766e+05, atom= 12585* * * *Step 8, time 0.008 (ps) LINCS WARNING* *relative constraint deviation after LINCS:* *rms 0.09, max 0.000105 (between atoms 12731 and 12728)* *bonds that rotated more than 30 degrees:* * atom 1 atom 2 angle previous, current, constraint length* * 12586 12585 32.10.0936 0.0936 0.0936* *Step=8, Dmax= 3.6e-02 nm, Epot= -8.55218e+05 Fmax= 5.79704e+04, atom= 12585* *Step=9, Dmax= 4.3e-02 nm, Epot= -8.92739e+05 Fmax= 1.11595e+05, atom= 12585* * * *Step 10, time 0.01 (ps) LINCS WARNING* *relative constraint deviation after LINCS:* *rms 0.45, max 0.000529 (between atoms 12731 and 12728)* *bonds that rotated more than 30 degrees:* * atom 1 atom 2 angle previous, current, constraint length* * 12586 12585 46.30.0934 0.0936 0.0936* * 12731 12730 31.30.0936 0.0936 0.0936* *Step= 10, Dmax= 5.2e-02 nm, Epot= -9.06732e+05 Fmax= 8.54476e+04, atom= 12730* * * *Step 11, time 0.011 (ps) LINCS WARNING* *relative constraint deviation after LINCS:* *rms 0.000184, max 0.002545 (between atoms 12731 and 12728)* *bonds that rotated more than 30 degrees:* * atom 1 atom 2 angle previous, current, constraint length* * 12731 12730 63.60.0936 0.0937 0.0936* *Step= 11, Dmax= 6.2e-02 nm, Epot= -9.23686e+05 Fmax= 1.13169e+05, atom= 15031* *Step= 12, Dmax= 7.4e-02 nm, Epot= -9.23888e+05 Fmax= 3.23226e+05, atom= 15031* * * *Step 13, time 0.013 (ps) LINCS WARNING* *relative constraint deviation after LINCS:* *rms 0.054250, max 0.852392 (between atoms 12731 and 12728)* *bonds that rotated more than 30 degrees:* * atom 1 atom 2 angle previous, current, constraint length* * 12736 12728 142.10.1908 0.1192 0.1681* * 12737 12728 146.10.1966 0.1354 0.1681* * * *Back Off! I just backed up step13b_n4.pdb to ./#step13b_n4.pdb.1#* * * *Back Off! I just backed up step13c_n4.pdb to ./#step13c_n4.pdb.1#* *Wrote pdb files with previous and current coordinates* *Step= 13, Dmax= 8.9e-02 nm, Epot= -9.22947e+05 Fmax= 2.12030e+06, atom= 12728* *Step 14, time 0.014 (ps) LINCS WARNING* *relative constraint deviation after LINCS:* *rms 0.060515, max 0.946017 (between atoms 12731 and 12728)* *bonds that rotated more than 30 degrees:* * atom 1 atom 2 angle previous, current, constraint length* * 12736 12728 141.90.1908 0.1315 0.1681* * 12737 12728 149.50.1966 0.1435 0.1681* * * *Back Off! I just backed up step14b_n4.pdb to ./#step14b_n4.pdb.1#* * * *Back Off! I just backed up step14c_n4.pdb to ./#step14c_n4.pdb.1#* *Wrote pdb files with previous and current coordinates* *Step= 14, Dmax= 4.5e-02 nm, Epot= -9.25189e+05 Fmax= 2.68447e+06, atom= 12728* * * *Step 15, time 0.015 (ps) LINCS WARNING* *relative constraint deviation after LINCS:* *rms 1.882205, max 21.643097 (between atoms 12736 and 12728)* *bonds that rotated more than 30 degrees:* * atom 1 atom 2 angle previous, current, constraint length* * 12730 12728 173.70.3265 3.7204 0.1681* * 12731 12728 167.10.3272 3.6402 0.1681* * 12736 12728 159.70.1315 3.8068 0.1681* * 12737 12728 157.00.1435 3.7391 0.1681* * 12731 12730 48.90.0913 0.1124 0.0936* * 12737 12736 38.50.0960 0.1056 0.0936* * * *Back Off! I just backed up step15b_n4.pdb to ./#step15b_n4.pdb.1#* * * *Back Off! I just backed up step15c_n4.pdb to ./#step15c_n4.pdb.1#* *Wrote pdb files with previous and current coordinates* *Warning: 1-4 interaction between 12732 and 12741 at distance 1.975 which is larger than the 1-4 table size 1.800 nm* *These are ignored for the rest of the simulation* *This usually means your system is exploding,* *if not, you should increase table-extension in your mdp file* *or with user tables increase the table size* * * *A list of missing interactions:* * Connect Bonds of 7310 missing 1* *
Re: [gmx-users] Re: Gromacs analysis tools for Namd output
Hu Paul, it is possible the dl library (containing the function to dinamically loading libraries) is missed. To confirm this hypotesis, try: ldd path_g_rmsf On my PC this is the output: linux-vdso.so.1 = (0x7fff6000) libgmxana.so.6 = /apps/gromacs/4.5.5/gnu/lib/libgmxana.so.6 (0x7f6e50994000) libmd.so.6 = /apps/gromacs/4.5.5/gnu/lib/libmd.so.6 (0x7f6e50529000) libxml2.so.2 = /usr/lib/libxml2.so.2 (0x7f6e501a9000) libgmx.so.6 = /apps/gromacs/4.5.5/gnu/lib/libgmx.so.6 (0x7f6e4fbe6000) *libdl.so.2 = /lib/x86_64-linux-gnu/libdl.so.2 (0x7f6e4f9e2000)* libnsl.so.1 = /lib/x86_64-linux-gnu/libnsl.so.1 (0x7f6e4f7c7000) libm.so.6 = /lib/x86_64-linux-gnu/libm.so.6 (0x7f6e4f542000) libpthread.so.0 = /lib/x86_64-linux-gnu/libpthread.so.0 (0x7f6e4f324000) libc.so.6 = /lib/x86_64-linux-gnu/libc.so.6 (0x7f6e4ef8f000) libz.so.1 = /lib/x86_64-linux-gnu/libz.so.1 (0x7f6e4ed77000) /lib64/ld-linux-x86-64.so.2 (0x7f6e50de2000) If you miss this library, try to instrall again gromacs including this library Francesco Il 07/02/2012 20:04, Kunze, Micha ha scritto: Hey Paul, cant help you with the plugin issue, but have you instead tried loading the dcd trajectory into vmd and save it as trr? Cheers, Micha On 7 Feb 2012, at 18:18, PAUL NEWMAN paulcliz...@gmail.com mailto:paulcliz...@gmail.com wrote: Dear Gromacs users, This is my second email since I tried the previous advises and did NOT work. I want to use the Gromacs analysis tools for analyzing Namd output files (*.dcd files) I installed Gromacs 4.5.4 (64 bits) and it works well. In addition I installed VMD 1.9 (64 bits) and set up VMD_PLUGIN_PATH=/home/vmd-1.9/plugins/LINUXAMD64/molfile/ (Here it is located the dcdplugin.so ) I verified that VMD_PLUGIN_PATH is pointing out to the right folder. However when I run for example *g_rmsf_d -f file.dcd -s file.pdb * I got the following error *The file format of file.dcd is not a known trajectory format to GROMACS. Please make sure that the file is a trajectory! GROMACS will now assume it to be a trajectory and will try to open it using the VMD plug-ins.* * This will only work in case the VMD plugins are found and it is a trajectory format supported by VMD. No plugin for dcd found* Can anyone tell me if Gromacs really works with the VMD pulgin? I will highly appreciate to know it so I can start looking for another alternatives. Thanks so much -- Cheers, Paul -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Using groups in the mdp file
Hi Ignacio, You can solve the problem creating an index file through make_ndx. In such a file you need a group called ACX. Then use the index.ndx in grompp. Francesco 2012/2/6, Ignacio Fernández Galván jel...@yahoo.com: Hi all, I have a system with a molecule called ACX plus water (molecules called SOL), but when I try to use ACX as a group name in the .mdp file, grompp says such a group does not exist: --- Program grompp, VERSION 4.5.5 Source code file: readir.c, line: 1320 Fatal error: Group ACX not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- However, the .top file is, I believe, correct, it contains these lines: [ moleculetype ] ; Namenrexcl ACX 3 and then [atoms], [bonds], etc. It ends with: [ molecules ] ; Compound#mols ACX 1 SOL 2139 and that's not a problem. It's when I try to use ACX as a group name, as in: energy_grps = ACX that I get the error. What am I doing wrong? Is there any option I must activate to enable using molecule names as groups? Thanks, Ignacio -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] high forces
Dear gromacs users, I am attempting to simulate a protein with an active site containing to metals (Ni and Fe). I am trying to mantain the active site structure constraining bonds, angles and dihedrals. When I simulate the active site alone in water, it remains stable. When I insert the active site in the protein's scaffold, unfortunately, the simulation crashes because of large vibration in bond lenght and angle amplitude in the active site. I am not able to detect big clashes or any structural distortion. I tried to play with force constants, temperature, time-step, constrains, etc.etc. but I am not able to mantain the simulation stability. I am wondering whether exists a tool to dissect the energetic contributions ( including bonded parameters ) permitting me to identify the problem giving rise the crash. Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] dihedral
Dear gromacs users, I'm trying to restrain the value of a particular dihedral using the section [ dihedral_restraints ] : [ dihedral_restraints ] ; ai ajakaltypelabel phi dphi kfac power 13919 13915 13921 139221 1 -67.19 0 14 I ran an energy minimization through mdrun_d -deffnm 01em -v -debug 6 but, unfortunately, the values are far from the wanted value ( in radians -67.19 = -1.17) as grep reveals: grep dihres mdrun_d.debug dihres[0]: 12650 12647 12651 12652 : phi=-1.090441, dphi=0.00, kfac=100.00, power=4, label=1 dihres[0]: 12650 12647 12651 12652 : phi=-1.090497, dphi=0.00, kfac=100.00, power=4, label=1 dihres[0]: 12650 12647 12651 12652 : phi=-1.090586, dphi=0.00, kfac=100.00, power=4, label=1 dihres[0]: 12650 12647 12651 12652 : phi=-1.090734, dphi=0.00, kfac=100.00, power=4, label=1 dihres[0]: 12650 12647 12651 12652 : phi=-1.090996, dphi=0.00, kfac=100.00, power=4, label=1 dihres[0]: 12650 12647 12651 12652 : phi=-1.091487, dphi=0.00, kfac=100.00, power=4, label=1 dihres[0]: 12650 12647 12651 12652 : phi=-1.092475, dphi=0.00, kfac=100.00, power=4, label=1 dihres[0]: 12650 12647 12651 12652 : phi=-1.094620, dphi=0.00, kfac=100.00, power=4, label=1 dihres[0]: 12650 12647 12651 12652 : phi=-1.099689, dphi=0.00, kfac=100.00, power=4, label=1 dihres[0]: 12650 12647 12651 12652 : phi=-1.112823, dphi=0.00, kfac=100.00, power=4, label=1 dihres[0]: 12650 12647 12651 12652 : phi=-1.147934, dphi=0.00, kfac=100.00, power=4, label=1 dihres[0]: 12650 12647 12651 12652 : phi=-1.230998, dphi=0.00, kfac=100.00, power=4, label=1 dihres[0]: 12650 12647 12651 12652 : phi=-0.342237, dphi=0.00, kfac=100.00, power=4, label=1 dihres[0]: 12650 12647 12651 12652 : phi=-1.931253, dphi=0.00, kfac=100.00, power=4, label=1 dihres[0]: 12650 12647 12651 12652 : phi=1.093490, dphi=0.00, kfac=100.00, power=4, label=1 dihres[0]: 12650 12647 12651 12652 : phi=-0.846042, dphi=0.00, kfac=100.00, power=4, label=1 dihres[0]: 12650 12647 12651 12652 : phi=1.893053, dphi=0.00, kfac=100.00, power=4, label=1 dihres[0]: 12649 12646 12650 12651 : phi=-0.523006, dphi=0.00, kfac=100.00, power=4, label=1 dihres[0]: 12649 12646 12650 12651 : phi=2.245932, dphi=0.00, kfac=100.00, power=4, label=1 dihres[0]: 12649 12646 12650 12651 : phi=-1.518727, dphi=0.00, kfac=100.00, power=4, label=1 dihres[0]: 12649 12646 12650 12651 : phi=1.665189, dphi=0.00, kfac=100.00, power=4, label=1 dihres[0]: 12648 12645 12649 12650 : phi=-1.820232, dphi=0.00, kfac=100.00, power=4, label=1 dihres[0]: 12648 12645 12649 12650 : phi=1.414995, dphi=0.00, kfac=100.00, power=4, label=1 dihres[0]: 12648 12645 12649 12650 : phi=-2.154156, dphi=0.00, kfac=100.00, power=4, label=1 Do I made any error or did I miss something? The .top, .pdb and .mdp files to reproduce my problem can be downloaded from http://160.80.35.105/download/ Since there are same not-standard residues, I've attacched the file obtained using the option -pp in grompp. Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Cosine content
Hi Vijayan, cosine content should say how not-random are the movements observed in the configuration set you have analized. Regarding your case, this means that, even if the RMSD is stable starting from 5ns, the protein still experiences random motions. You should therefore consider as statistically relevant the trajectory starting from 30ns. Basing on my experience, I advice you to extend the simulation lenght (i.e.100ns) to ensure a larger dataset. Francesco Il 14/12/2011 00:37, R.S.K.Vijayan ha scritto: Dear Gromacs users I have a question regarding cosine content. I have a 50 ns trajectory and looking at the RMSD plot, i set aside the first 5 ns as the time required for stabilization and subsequently carried out a essential dynamics for the backbone atoms post 5ns. But when i perform a cosine content analysis for the eigen vector 1, i get these strange results a) Performing a g_analyze run using -b 5000 to -e 5 ( ie 5- 50 ns ) produces a cosine value of 0.92 but when i perform a cosine analysis using -b 5000 to -e 25000 ( 5-25ns) i get a cosine value of 0.24 also when i perform a cosine analysis using -b 3 to -- 5(30-50 ns) i get a cosine value of 0.05 so how should i interpret this result, does it imply that all the conformational changes are taking place between 30 to 50 ns or is there some thing wrong with the convergence of the system??? Papers tell that the cosine value does decreases with increased time scale due to enhanced sampling, but strange a 25 ns simulation has a low cosine value on the contrary a 50 ns simulation has an increased cosine value. Regards Vijayan.R On Mon, Dec 12, 2011 at 5:31 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Alex Jemulin wrote: Dear all Which is the difference between hydropilic and hydrophobic sas? g_sas computes hydrophobic and hydrophilic surface area based on the absolute value of the partial charge of the atom, which can be adjusted with the -qmax flag. How can give an interpretation to g_sas xvg graph? Interpretation of the results is based on the question being asked and the group being analyzed, things that only you know. What can I find out in it and how can use g_sas to analyze a trajectory? Start by reading g_sas -h. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] unity in ffbonded.itp
Dear gromacs developers, I would like to know what is the unity for armonic constraint in ffbonded.itp. In the user manual (Table 5.4) it is written that is kJ mol-1 nm-2 but in the .itp file I read C C 1 0.1525 259408.0 ; new99 I understand that 0.1525 is the equlibrium distance 5in nm) but 259408.0 KJ it is almost high. Maybe the right value is 259408.0 J ? Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] removing dihedral
Dear gromacs users, I am trying to build the topology for a protein-ligands system. When I run grompp I obtain 96 of the following errors: ERROR 1 [file topol_Protein_chain_S.itp, line 38658]: No default Proper Dih. types The errors correctly says that dihedral parameters are missing for my ligands. My question is, there is a method to avoid considering such a dihedrals, avoiding topology editing? In other words, I don't wanna edit the .top file removing by-hand the lines generating the error. Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] removing dihedral
I am using parameters already developed for CHARMM. So I guess the parameters are right and I am sure there is no error in the trasformation from CHARMM to GROMACS format. May the option -zero in grompp solve my problem? Il 21/11/2011 21:00, Justin A. Lemkul ha scritto: francesco oteri wrote: Dear gromacs users, I am trying to build the topology for a protein-ligands system. When I run grompp I obtain 96 of the following errors: ERROR 1 [file topol_Protein_chain_S.itp, line 38658]: No default Proper Dih. types The errors correctly says that dihedral parameters are missing for my ligands. My question is, there is a method to avoid considering such a dihedrals, avoiding topology editing? In other words, I don't wanna edit the .top file removing by-hand the lines generating the error. If you're missing parameters, you need to assign them. Whether or not that requires deriving new dihedral types depends on the complexity of the molecule. -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] removing dihedral
ffbonded.itp is right, grompp misses only a particular dihedral. Everithing is fine for bond, angle and some dihedrals. What exactly means zeroing out all terms for the unknown dihedrals? It means that are not present in tpr or that parameters (i.e reference angle, multiplicity,...) are zero? Il 21/11/2011 21:21, Justin A. Lemkul ha scritto: Francesco Oteri wrote: I am using parameters already developed for CHARMM. So I guess the parameters are right and I am sure there is no error in the trasformation from CHARMM to GROMACS format. May the option -zero in grompp solve my problem? Well, using grompp -zero will bypass the error by zeroing out all terms for the unknown dihedrals. If there are 96 of them, that means you will have completely incorrect bonded interactions. If you have parameters that should work for this particular molecule, they are not being found in ffbonded.itp. That's the problem. So you can resolve the problem by adding bonded parameters to that file or defining them locally in your .top with a suitably placed [dihedrals] (or whatever else) directive. -Justin Il 21/11/2011 21:00, Justin A. Lemkul ha scritto: francesco oteri wrote: Dear gromacs users, I am trying to build the topology for a protein-ligands system. When I run grompp I obtain 96 of the following errors: ERROR 1 [file topol_Protein_chain_S.itp, line 38658]: No default Proper Dih. types The errors correctly says that dihedral parameters are missing for my ligands. My question is, there is a method to avoid considering such a dihedrals, avoiding topology editing? In other words, I don't wanna edit the .top file removing by-hand the lines generating the error. If you're missing parameters, you need to assign them. Whether or not that requires deriving new dihedral types depends on the complexity of the molecule. -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] ZN charge
Dear gromacs users, I am inspecting the charmm27.ff/ions.itp file and I noticed that the ZN ion has a negative charge: [ moleculetype ] ; molname nrexcl ZN 1 [ atoms ] ; idat type res nr residu name at name cg nr charge 1 ZN 1 ZN ZN 1 -2 Is it right? -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] protein-water distance restraints
Dear Markus, If you know the residues composing the cavity (and I think you know it), you can simply change the coordinates of the water molecule in the .gro file to move the water in the cavity. Francesco Il 12/10/2011 18:17, Markus Weingarth ha scritto: Dear Gromacs-users, I would like to force an arbitrary water molcule from the box into an occluded cavity of a membrane-channel. It do not want this water molcule within the cavity at the beginning of the simulation. I though that I could implement intermolecular distance restraints between a water residue an the protein, but I did not manage that and all the suggestions I found here to implement intermolecular distance restraints seem not to work out for water - protein contacts. Does anybody has a suggestion how to implement such restraints ? Would the pull-code an option for my problem ? Thank you very much Markus SMS schreiben mit WEB.DE FreeMail - einfach, schnell und kostenguenstig. Jetzt gleich testen! *http://f.web.de/?mc=021192* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] iron sulphur cluster
Dear gromacs users, I've to simulate a protein with an 4Fe-4S and a 3Fe-4S iron sulphur cluster. Lot of approaches are present in literature. There are a lot of papaers suggesting partial charges but very few suggestions regarding bonded and not bonded parameters. So i am wondering if any member of this mailing list can send me a link, a file or something advice can be useful to obtain the topology of a protein with the iron sulphur clusters. It is worth noting that I am not interested in electronic properties so also advice using restraint are ok for me. Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] iron sulphur cluster
The author of such work published partial charges, but nothing about other parameters. The force-fields used are gromos43A1 and CHARMM22. The GROMACS standard distribution contains nothing about iron sulphur cluster. Thank you 2011/10/6 Mark Abraham mark.abra...@anu.edu.au On 6/10/2011 11:24 PM, francesco oteri wrote: Dear gromacs users, I've to simulate a protein with an 4Fe-4S and a 3Fe-4S iron sulphur cluster. Lot of approaches are present in literature. There are a lot of papaers suggesting partial charges but very few suggestions regarding bonded and not bonded parameters. All such work should describe a source for such parameters, if they are not in the standard force field. So i am wondering if any member of this mailing list can send me a link, a file or something advice can be useful to obtain the topology of a protein with the iron sulphur clusters. It is worth noting that I am not interested in electronic properties so also advice using restraint are ok for me. The authors of such work would be a good place to ask. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_cluster -dm option
Hi santhu, maybe the differecence you observed depend by the xpm format. In the xpm each cell is represented by one character that, in turn, is represented as a color by xpm2ps. Therefore the character count cannot be infinite so each character can represent a range of RMSD cell. In my opinion this rapresentation is the source of the problem. You should modify g_cluster to write the RMSD matrix in a binary format to avoid rounding error and, at the same time, to save computational time. Il 29/09/2011 22:25, santhu kumar ha scritto: Hello, I am using g_cluster to cluster trajectories. The exact command I am using is : g_cluster -s protein.pdb -f all.trr -n index.ndx -o rmsd-clust.xpm -method gromos -cutoff 0.07 -wcl 250. This command gives me 145 clusters. This command writes out a rmsd-clust.xpm, which is the RMSD distance matrix. Since the trajectory is quite huge, i want to perform the RMSD matrix computation only once. If I want to change options of clustering, I have tried giving the computed matrix as input to another run but the results are quite different. For example : g_cluster -s ubqs.pdb -f all.trr -n index.ndx -dm rmsd-clust.xpm -method gromos -cutoff 0.07 -wcl 250 would then give only 3 clusters. Can somebody please advice me on how to avoid recomputing the RMSD distance matrix for each change in clustering option?? Thanks Santhosh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Poisson-Boltzmann free energy in gromacs?
Hi Sanku, you can use APBS (Adaptive Poisson-Boltzman Solver, http://www.poissonboltzmann.org/apbs/ ). This program computes the PB equation on a single conformation, but you can write a script to calculate values over trajectory. APBS has the advances to be integrated into VMD and pymol, moreover is avalaible an MPI parallelized version. Francesco Il 17/07/2011 02:47, Mark Abraham ha scritto: On 17/07/2011 10:45 AM, Justin A. Lemkul wrote: Sanku M wrote: I thought since the implicit solvent model has been invoked recently, there might be some features for PB calculation as well. You can get GB polarization energies with the implicit solvent code, but not PB, as far as I am aware. If there are undocumented features, perhaps one of the developers can comment. But given the lack of any documentation on the matter, I would conclude that direct PB calculations cannot be done at present. They can't Mark -Justin *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Sat, July 16, 2011 7:35:43 PM *Subject:* Re: [gmx-users] Poisson-Boltzmann free energy in gromacs? Sanku M wrote: Hi, I was wondering whether, in gromacs, there is any way of calculating the electrostatic free energy using poisson Boltzmann equation. There is no mention of such a feature in the manual, so I would suspect the answer is no. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Water-Mediated Hydrogen Bonds
Hi Raja, You can perform the job calculating h-bond between Protein and Water and between DNA and Water. Now you have to select water that, in the same frame, form h-bond with protein and DNA. The residue information can be found in hbmap.xpm e hbond.log files. There is a perl script in the Justin's webpage (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/Scripts/plot_hbmap.txt) that extract information from this files. You should modify it to reach your goal Francesco Il 04/07/2011 17:02, Erik Marklund ha scritto: -ins doesn't work as far as I know, and I believe the help text says so. Erik 2 jul 2011 kl. 08.31 skrev Raja Pandian: Dear All, I’m doing research in the field of Protein-DNA interaction. I have gone through these papers, *A “Solvated Rotamer” Approach to Modeling Water-Mediated Hydrogen Bonds at Protein–Protein Interfaces* *“Effect on DNA relaxation of the single Thr718Ala mutation in human topoisomerase I: a functional and molecular dynamics study”* *“Molecular Dynamics Simulation Study of Interaction between Model Rough Hydrophobic Surfaces.”* *“Prediction of Protein Binding to DNA in the Presence of Water-Mediated Hydrogen Bonds”* I have found lot of interesting things on these papers that will be useful for the progress of my research carrier. I have been looking for water mediated hydrogen bond in my simulation when iuse g_hbond the -ins option it dose not showing the water mediated hydrogen bond could you please tell me how to get the hydrogen mediated hydrogen bond and water mediated free energy in Gromacs ? Is there any way to calculate water mediated hydrogen bond between Protein-DNA using Gromacs tools? If it is possible, please send your program (water mediated hydrogen bond derivation program) to me and also the program operating procedure. Eagerly waiting for your reply. Thanking You Faithfully Raja -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.se mailto:er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
